R Notebook

Test one: Check if BiocManager is valid

library(BiocManager)

BiocManager::valid()

5 packages out-of-date; 0 packages too new

* sessionInfo()

R version 3.6.1 (2019-07-05)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default
BLAS/LAPACK: /usr/lib/libopenblasp-r0.2.19.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8       
 [4] LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=C             
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C              
[10] LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] BiocManager_1.30.10

loaded via a namespace (and not attached):
 [1] compiler_3.6.1  magrittr_1.5    htmltools_0.4.0 tools_3.6.1     base64enc_0.1-3
 [6] yaml_2.2.0      Rcpp_1.0.3      stringi_1.4.3   rmarkdown_1.18  knitr_1.26     
[11] jsonlite_1.6    stringr_1.4.0   digest_0.6.23   xfun_0.11       rlang_0.4.2    
[16] evaluate_0.14  

Bioconductor version '3.10'

  * 5 packages out-of-date
  * 0 packages too new

create a valid installation with

  BiocManager::install(c(
    "callr", "cli", "data.table", "RSQLite", "rversions"
  ), update = TRUE, ask = FALSE)

more details: BiocManager::valid()$too_new, BiocManager::valid()$out_of_date

Test 2: Update the packages

  BiocManager::install(c(
    "callr", "cli", "data.table", "RSQLite", "rversions"
  ), update = TRUE, ask = FALSE)

Bioconductor version 3.10 (BiocManager 1.30.10), R 3.6.1 (2019-07-05)
Installing package(s) 'callr', 'cli', 'data.table', 'RSQLite', 'rversions'
trying URL 'https://cran.rstudio.com/src/contrib/callr_3.4.0.tar.gz'
Content type 'application/x-gzip' length 100129 bytes (97 KB)
==================================================
downloaded 97 KB

trying URL 'https://cran.rstudio.com/src/contrib/cli_2.0.0.tar.gz'
Content type 'application/x-gzip' length 111873 bytes (109 KB)
==================================================
downloaded 109 KB

trying URL 'https://cran.rstudio.com/src/contrib/data.table_1.12.8.tar.gz'
Content type 'application/x-gzip' length 4948391 bytes (4.7 MB)
==================================================
downloaded 4.7 MB

trying URL 'https://cran.rstudio.com/src/contrib/RSQLite_2.1.4.tar.gz'
Content type 'application/x-gzip' length 2360758 bytes (2.3 MB)
==================================================
downloaded 2.3 MB

trying URL 'https://cran.rstudio.com/src/contrib/rversions_2.0.1.tar.gz'
Content type 'application/x-gzip' length 41476 bytes (40 KB)
==================================================
downloaded 40 KB

* installing *source* package ‘callr’ ...
** package ‘callr’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (callr)
* installing *source* package ‘cli’ ...
** package ‘cli’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (cli)
* installing *source* package ‘data.table’ ...
** package ‘data.table’ successfully unpacked and MD5 sums checked
** using staged installation

zlib 1.2.8 is available ok

** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c assign.c -o assign.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c between.c -o between.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bmerge.c -o bmerge.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chmatch.c -o chmatch.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cj.c -o cj.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coalesce.c -o coalesce.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dogroups.c -o dogroups.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastmean.c -o fastmean.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fcast.c -o fcast.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fifelse.c -o fifelse.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fmelt.c -o fmelt.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c forder.c -o forder.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frank.c -o frank.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fread.c -o fread.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c freadR.c -o freadR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c froll.c -o froll.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frollR.c -o frollR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frolladaptive.c -o frolladaptive.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fsort.c -o fsort.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fwrite.c -o fwrite.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fwriteR.c -o fwriteR.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gsumm.c -o gsumm.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ijoin.c -o ijoin.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inrange.c -o inrange.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nafill.c -o nafill.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nqrecreateindices.c -o nqrecreateindices.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c openmp-utils.c -o openmp-utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c quickselect.c -o quickselect.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rbindlist.c -o rbindlist.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c reorder.c -o reorder.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c shift.c -o shift.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subset.c -o subset.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transpose.c -o transpose.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c types.c -o types.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c uniqlist.c -o uniqlist.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vecseq.c -o vecseq.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c wrappers.c -o wrappers.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o data.table.so assign.o between.o bmerge.o chmatch.o cj.o coalesce.o dogroups.o fastmean.o fcast.o fifelse.o fmelt.o forder.o frank.o fread.o freadR.o froll.o frollR.o frolladaptive.o fsort.o fwrite.o fwriteR.o gsumm.o ijoin.o init.o inrange.o nafill.o nqrecreateindices.o openmp-utils.o quickselect.o rbindlist.o reorder.o shift.o subset.o transpose.o types.o uniqlist.o utils.o vecseq.o wrappers.o -fopenmp -lz -L/usr/local/lib/R/lib -lR
mv data.table.so datatable.so
if [ "" != "Windows_NT" ] && [ `uname -s` = 'Darwin' ]; then install_name_tool -id datatable.so datatable.so; fi

installing to /usr/local/lib/R/site-library/00LOCK-data.table/00new/data.table/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (data.table)
* installing *source* package ‘RSQLite’ ...
** package ‘RSQLite’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbColumn.cpp -o DbColumn.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbColumnDataSource.cpp -o DbColumnDataSource.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbColumnDataSourceFactory.cpp -o DbColumnDataSourceFactory.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbColumnStorage.cpp -o DbColumnStorage.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbConnection.cpp -o DbConnection.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbDataFrame.cpp -o DbDataFrame.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DbResult.cpp -o DbResult.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteColumnDataSource.cpp -o SqliteColumnDataSource.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteColumnDataSourceFactory.cpp -o SqliteColumnDataSourceFactory.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteDataFrame.cpp -o SqliteDataFrame.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteResult.cpp -o SqliteResult.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SqliteResultImpl.cpp -o SqliteResultImpl.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c affinity.c -o affinity.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c connection.cpp -o connection.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c extension-functions.c -o extension-functions.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c extensions.cpp -o extensions.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c import-file.c -o import-file.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c regexp.c -o regexp.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c result.cpp -o result.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rsqlite.cpp -o rsqlite.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -I. -DRSQLITE_USE_BUNDLED_SQLITE -DSQLITE_ENABLE_RTREE -DSQLITE_ENABLE_FTS3 -DSQLITE_ENABLE_FTS3_PARENTHESIS -DSQLITE_ENABLE_FTS5 -DSQLITE_ENABLE_JSON1 -DSQLITE_ENABLE_STAT4 -DSQLITE_SOUNDEX -DRCPP_DEFAULT_INCLUDE_CALL=false -DRCPP_USING_UTF8_ERROR_STRING -DBOOST_NO_AUTO_PTR -I"/usr/local/lib/R/site-library/BH/include" -I"/usr/local/lib/R/site-library/plogr/include" -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vendor/sqlite3/sqlite3.c -o vendor/sqlite3/sqlite3.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RSQLite.so DbColumn.o DbColumnDataSource.o DbColumnDataSourceFactory.o DbColumnStorage.o DbConnection.o DbDataFrame.o DbResult.o RcppExports.o SqliteColumnDataSource.o SqliteColumnDataSourceFactory.o SqliteDataFrame.o SqliteResult.o SqliteResultImpl.o affinity.o connection.o extension-functions.o extensions.o import-file.o regexp.o result.o rsqlite.o vendor/sqlite3/sqlite3.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-RSQLite/00new/RSQLite/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RSQLite)
* installing *source* package ‘rversions’ ...
** package ‘rversions’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rversions)

The downloaded source packages are in
    ‘/tmp/Rtmp9iAvbX/downloaded_packages’
Installation path not writeable, unable to update packages: boot, foreign, KernSmooth, Matrix,
  mgcv, nlme, survival

Now check again if BiocManager is valid

BiocManager::valid()

[1] TRUE

What are the available .libPaths()

.libPaths()

[1] "/usr/local/lib/R/site-library" "/usr/local/lib/R/library"     

What are the packages on the .libPaths()

sapply(seq(.libPaths()),function(x) rownames(installed.packages(.libPaths()[x])))

[[1]]
  [1] "askpass"             "assertthat"          "backports"           "base64enc"          
  [5] "BH"                  "bigrquery"           "BiocManager"         "BiocVersion"        
  [9] "bit"                 "bit64"               "bitops"              "blob"               
 [13] "brew"                "broom"               "callr"               "caTools"            
 [17] "cellranger"          "cli"                 "clipr"               "clisymbols"         
 [21] "colorspace"          "commonmark"          "covr"                "crayon"             
 [25] "crosstalk"           "curl"                "cyclocomp"           "data.table"         
 [29] "DBI"                 "dbplyr"              "desc"                "devtools"           
 [33] "digest"              "docopt"              "dplyr"               "DT"                 
 [37] "dtplyr"              "ellipsis"            "evaluate"            "fansi"              
 [41] "farver"              "fastmap"             "feather"             "foghorn"            
 [45] "forcats"             "formatR"             "fs"                  "gargle"             
 [49] "generics"            "ggplot2"             "gh"                  "git2r"              
 [53] "glue"                "gmailr"              "googleAuthR"         "googleCloudStorageR"
 [57] "gtable"              "haven"               "highlight"           "highr"              
 [61] "hms"                 "htmltools"           "htmlwidgets"         "httpuv"             
 [65] "httr"                "hunspell"            "ini"                 "jsonlite"           
 [69] "knitr"               "labeling"            "Lahman"              "later"              
 [73] "lazyeval"            "lifecycle"           "lintr"               "littler"            
 [77] "lubridate"           "magrittr"            "markdown"            "memoise"            
 [81] "microbenchmark"      "mime"                "mockery"             "modelr"             
 [85] "munsell"             "nycflights13"        "openssl"             "parsedate"          
 [89] "pillar"              "pingr"               "pkgbuild"            "pkgconfig"          
 [93] "pkgdown"             "pkgload"             "plogr"               "plyr"               
 [97] "praise"              "prettyunits"         "processx"            "progress"           
[101] "promises"            "ps"                  "purrr"               "R6"                 
[105] "rapidjsonr"          "rappdirs"            "rcmdcheck"           "RColorBrewer"       
[109] "Rcpp"                "readr"               "readxl"              "rematch"            
[113] "rematch2"            "remotes"             "reprex"              "reshape2"           
[117] "rex"                 "rhub"                "rlang"               "rmarkdown"          
[121] "RMySQL"              "Ronaldo"             "roxygen2"            "RPostgreSQL"        
[125] "rprojroot"           "RSQLite"             "rstudioapi"          "rversions"          
[129] "rvest"               "scales"              "selectr"             "sessioninfo"        
[133] "shiny"               "sourcetools"         "spelling"            "stringdist"         
[137] "stringi"             "stringr"             "sys"                 "testit"             
[141] "testthat"            "tibble"              "tidyr"               "tidyselect"         
[145] "tidyverse"           "tinytex"             "usethis"             "utf8"               
[149] "uuid"                "vctrs"               "viridisLite"         "whisker"            
[153] "whoami"              "withr"               "xfun"                "XML"                
[157] "xml2"                "xmlparsedata"        "xopen"               "xtable"             
[161] "yaml"                "zeallot"             "zip"                

[[2]]
 [1] "base"       "boot"       "class"      "cluster"    "codetools"  "compiler"   "datasets"  
 [8] "foreign"    "graphics"   "grDevices"  "grid"       "KernSmooth" "lattice"    "MASS"      
[15] "Matrix"     "methods"    "mgcv"       "nlme"       "nnet"       "parallel"   "rpart"     
[22] "spatial"    "splines"    "stats"      "stats4"     "survival"   "tcltk"      "tools"     
[29] "utils"     

BUG 1

Need to move “recommended packages” need to go into /usr/local/lib/R/site-library.

Check if “core” packages install

• to make this image similar to terra-jupyter-bioconductor image.

• install(c(
  “SingleCellExperiment”,
  “GenomicFeatures”,
  “GenomicAlignments”,
  “ShortRead”,
  “DESeq2”))’

BiocManager::install(c(
    "SingleCellExperiment",
    "GenomicFeatures", 
    "GenomicAlignments", 
    "ShortRead", 
    "DESeq2"))

trying URL 'https://cran.rstudio.com/src/contrib/matrixStats_0.55.0.tar.gz'
Content type 'application/x-gzip' length 187479 bytes (183 KB)
==================================================
downloaded 183 KB

trying URL 'https://cran.rstudio.com/src/contrib/lambda.r_1.2.4.tar.gz'
Content type 'application/x-gzip' length 25666 bytes (25 KB)
==================================================
downloaded 25 KB

trying URL 'https://cran.rstudio.com/src/contrib/futile.options_1.0.1.tar.gz'
Content type 'application/x-gzip' length 3919 bytes
==================================================
downloaded 3919 bytes

trying URL 'https://cran.rstudio.com/src/contrib/checkmate_1.9.4.tar.gz'
Content type 'application/x-gzip' length 214038 bytes (209 KB)
==================================================
downloaded 209 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/DelayedArray_0.12.0.tar.gz'
Content type 'application/x-gzip' length 552513 bytes (539 KB)
==================================================
downloaded 539 KB

trying URL 'https://bioconductor.org/packages/3.10/data/annotation/src/contrib/GenomeInfoDbData_1.2.2.tar.gz'
Content type 'application/x-gzip' length 10194482 bytes (9.7 MB)
==================================================
downloaded 9.7 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocFileCache_1.10.2.tar.gz'
Content type 'application/x-gzip' length 288347 bytes (281 KB)
==================================================
downloaded 281 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rhtslib_1.18.0.tar.gz'
Content type 'application/x-gzip' length 1471164 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'https://cran.rstudio.com/src/contrib/futile.logger_1.4.3.tar.gz'
Content type 'application/x-gzip' length 17456 bytes (17 KB)
==================================================
downloaded 17 KB

trying URL 'https://cran.rstudio.com/src/contrib/snow_0.4-3.tar.gz'
Content type 'application/x-gzip' length 22675 bytes (22 KB)
==================================================
downloaded 22 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/annotate_1.64.0.tar.gz'
Content type 'application/x-gzip' length 1873132 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://cran.rstudio.com/src/contrib/Formula_1.2-3.tar.gz'
Content type 'application/x-gzip' length 151340 bytes (147 KB)
==================================================
downloaded 147 KB

trying URL 'https://cran.rstudio.com/src/contrib/acepack_1.4.1.tar.gz'
Content type 'application/x-gzip' length 34848 bytes (34 KB)
==================================================
downloaded 34 KB

trying URL 'https://cran.rstudio.com/src/contrib/gridExtra_2.3.tar.gz'
Content type 'application/x-gzip' length 1062844 bytes (1.0 MB)
==================================================
downloaded 1.0 MB

trying URL 'https://cran.rstudio.com/src/contrib/htmlTable_1.13.3.tar.gz'
Content type 'application/x-gzip' length 173116 bytes (169 KB)
==================================================
downloaded 169 KB

trying URL 'https://cran.rstudio.com/src/contrib/viridis_0.5.1.tar.gz'
Content type 'application/x-gzip' length 1906320 bytes (1.8 MB)
==================================================
downloaded 1.8 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/SummarizedExperiment_1.16.0.tar.gz'
Content type 'application/x-gzip' length 1517919 bytes (1.4 MB)
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downloaded 1.4 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/S4Vectors_0.24.1.tar.gz'
Content type 'application/x-gzip' length 651246 bytes (635 KB)
==================================================
downloaded 635 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocGenerics_0.32.0.tar.gz'
Content type 'application/x-gzip' length 46806 bytes (45 KB)
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downloaded 45 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/IRanges_2.20.1.tar.gz'
Content type 'application/x-gzip' length 463779 bytes (452 KB)
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downloaded 452 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomeInfoDb_1.22.0.tar.gz'
Content type 'application/x-gzip' length 3409309 bytes (3.3 MB)
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downloaded 3.3 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/GenomicRanges_1.38.0.tar.gz'
Content type 'application/x-gzip' length 1169872 bytes (1.1 MB)
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downloaded 1.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/AnnotationDbi_1.48.0.tar.gz'
Content type 'application/x-gzip' length 4338899 bytes (4.1 MB)
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downloaded 4.1 MB

trying URL 'https://cran.rstudio.com/src/contrib/RCurl_1.95-4.12.tar.gz'
Content type 'application/x-gzip' length 916763 bytes (895 KB)
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downloaded 895 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/XVector_0.26.0.tar.gz'
Content type 'application/x-gzip' length 66028 bytes (64 KB)
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downloaded 64 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Biostrings_2.54.0.tar.gz'
Content type 'application/x-gzip' length 12708673 bytes (12.1 MB)
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downloaded 12.1 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/rtracklayer_1.46.0.tar.gz'
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downloaded 1.5 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/biomaRt_2.42.0.tar.gz'
Content type 'application/x-gzip' length 432052 bytes (421 KB)
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downloaded 421 KB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Biobase_2.46.0.tar.gz'
Content type 'application/x-gzip' length 1657663 bytes (1.6 MB)
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downloaded 1.6 MB

trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/Rsamtools_2.2.1.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/BiocParallel_1.20.0.tar.gz'
Content type 'application/x-gzip' length 932190 bytes (910 KB)
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trying URL 'https://cran.rstudio.com/src/contrib/hwriter_1.3.2.tar.gz'
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trying URL 'https://bioconductor.org/packages/3.10/bioc/src/contrib/zlibbioc_1.32.0.tar.gz'
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* installing *source* package ‘matrixStats’ ...
** package ‘matrixStats’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c 000.init.c -o 000.init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c allocMatrix2.c -o allocMatrix2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c binCounts.c -o binCounts.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c binMeans.c -o binMeans.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colCounts.c -o colCounts.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colOrderStats.c -o colOrderStats.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c colRanges.c -o colRanges.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c diff2.c -o diff2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c indexByRow.c -o indexByRow.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c logSumExp.c -o logSumExp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mean2.c -o mean2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c productExpSumLog.c -o productExpSumLog.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c psortKM.c -o psortKM.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowCounts.c -o rowCounts.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowCummaxs.c -o rowCummaxs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowCummins.c -o rowCummins.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowCumprods.c -o rowCumprods.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowCumsums.c -o rowCumsums.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowDiffs.c -o rowDiffs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowLogSumExp.c -o rowLogSumExp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMads.c -o rowMads.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMeans2.c -o rowMeans2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowOrderStats.c -o rowOrderStats.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowRanges.c -o rowRanges.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowRanksWithTies.c -o rowRanksWithTies.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowSums2.c -o rowSums2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowVars.c -o rowVars.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c signTabulate.c -o signTabulate.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sum2.c -o sum2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c validateIndices.c -o validateIndices.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c weightedMean.c -o weightedMean.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c weightedMedian.c -o weightedMedian.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c x_OP_y.c -o x_OP_y.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o matrixStats.so 000.init.o allocMatrix2.o anyMissing.o binCounts.o binMeans.o colCounts.o colOrderStats.o colRanges.o diff2.o indexByRow.o logSumExp.o mean2.o productExpSumLog.o psortKM.o rowCounts.o rowCummaxs.o rowCummins.o rowCumprods.o rowCumsums.o rowDiffs.o rowLogSumExp.o rowMads.o rowMeans2.o rowMedians.o rowOrderStats.o rowRanges.o rowRanksWithTies.o rowSums2.o rowVars.o signTabulate.o sum2.o validateIndices.o weightedMean.o weightedMedian.o x_OP_y.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-matrixStats/00new/matrixStats/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (matrixStats)
* installing *source* package ‘lambda.r’ ...
** package ‘lambda.r’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (lambda.r)
* installing *source* package ‘futile.options’ ...
** package ‘futile.options’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (futile.options)
* installing *source* package ‘checkmate’ ...
** package ‘checkmate’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c all_missing.c -o all_missing.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c any_infinite.c -o any_infinite.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c any_missing.c -o any_missing.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c any_nan.c -o any_nan.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c checks.c -o checks.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c find_min_nchar.c -o find_min_nchar.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c guess_type.c -o guess_type.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c helper.c -o helper.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c integerish.c -o integerish.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c is_sorted.c -o is_sorted.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c qassert.c -o qassert.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c which_first.c -o which_first.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o checkmate.so all_missing.o any_infinite.o any_missing.o any_nan.o checks.o find_min_nchar.o guess_type.o helper.o init.o integerish.o is_sorted.o qassert.o which_first.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-checkmate/00new/checkmate/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (checkmate)
* installing *source* package ‘GenomeInfoDbData’ ...
** using staged installation
** data
** inst
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDbData)
* installing *source* package ‘BiocFileCache’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocFileCache)
* installing *source* package ‘snow’ ...
** package ‘snow’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (snow)
* installing *source* package ‘Formula’ ...
** package ‘Formula’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Formula)
* installing *source* package ‘acepack’ ...
** package ‘acepack’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

gfortran  -fpic  -g -O2  -c ace.f -o ace.o
gfortran  -fpic  -g -O2  -c avas.f -o avas.o
gfortran  -fpic  -g -O2  -c rlsmo.f -o rlsmo.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o acepack.so ace.o avas.o rlsmo.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-acepack/00new/acepack/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (acepack)
* installing *source* package ‘gridExtra’ ...
** package ‘gridExtra’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (gridExtra)
* installing *source* package ‘BiocGenerics’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

Creating a new generic function for ‘append’ in package ‘BiocGenerics’
Creating a new generic function for ‘as.data.frame’ in package ‘BiocGenerics’
Creating a new generic function for ‘cbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘rbind’ in package ‘BiocGenerics’
Creating a new generic function for ‘do.call’ in package ‘BiocGenerics’
Creating a new generic function for ‘duplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘anyDuplicated’ in package ‘BiocGenerics’
Creating a new generic function for ‘eval’ in package ‘BiocGenerics’
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Creating a new generic function for ‘pmax.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘pmin.int’ in package ‘BiocGenerics’
Creating a new generic function for ‘Reduce’ in package ‘BiocGenerics’
Creating a new generic function for ‘Filter’ in package ‘BiocGenerics’
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Creating a new generic function for ‘Map’ in package ‘BiocGenerics’
Creating a new generic function for ‘Position’ in package ‘BiocGenerics’
Creating a new generic function for ‘get’ in package ‘BiocGenerics’
Creating a new generic function for ‘mget’ in package ‘BiocGenerics’
Creating a new generic function for ‘grep’ in package ‘BiocGenerics’
Creating a new generic function for ‘grepl’ in package ‘BiocGenerics’
Creating a new generic function for ‘is.unsorted’ in package ‘BiocGenerics’
Creating a new generic function for ‘lapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘sapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘mapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘match’ in package ‘BiocGenerics’
Creating a new generic function for ‘order’ in package ‘BiocGenerics’
Creating a new generic function for ‘paste’ in package ‘BiocGenerics’
Creating a new generic function for ‘rank’ in package ‘BiocGenerics’
Creating a new generic function for ‘rownames’ in package ‘BiocGenerics’
Creating a new generic function for ‘colnames’ in package ‘BiocGenerics’
Creating a new generic function for ‘union’ in package ‘BiocGenerics’
Creating a new generic function for ‘intersect’ in package ‘BiocGenerics’
Creating a new generic function for ‘setdiff’ in package ‘BiocGenerics’
Creating a new generic function for ‘sort’ in package ‘BiocGenerics’
Creating a new generic function for ‘table’ in package ‘BiocGenerics’
Creating a new generic function for ‘tapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘unique’ in package ‘BiocGenerics’
Creating a new generic function for ‘unsplit’ in package ‘BiocGenerics’
Creating a new generic function for ‘var’ in package ‘BiocGenerics’
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Creating a new generic function for ‘which.max’ in package ‘BiocGenerics’
Creating a new generic function for ‘which.min’ in package ‘BiocGenerics’
Creating a new generic function for ‘IQR’ in package ‘BiocGenerics’
Creating a new generic function for ‘mad’ in package ‘BiocGenerics’
Creating a new generic function for ‘xtabs’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterCall’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterApplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterEvalQ’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterExport’ in package ‘BiocGenerics’
Creating a new generic function for ‘clusterMap’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parApply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parRapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parCapply’ in package ‘BiocGenerics’
Creating a new generic function for ‘parLapplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘parSapplyLB’ in package ‘BiocGenerics’
Creating a new generic function for ‘basename’ in package ‘BiocGenerics’
Creating a new generic function for ‘dirname’ in package ‘BiocGenerics’

** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocGenerics)
* installing *source* package ‘RCurl’ ...
** package ‘RCurl’ successfully unpacked and MD5 sums checked
** using staged installation

checking for curl-config... /usr/bin/curl-config
checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking how to run the C preprocessor... gcc -E
Version has a libidn field
Version has CURLOPT_URL
Version has CURLINFO_EFFECTIVE_URL
Version has CURLINFO_RESPONSE_CODE
Version has CURLINFO_TOTAL_TIME
Version has CURLINFO_NAMELOOKUP_TIME
Version has CURLINFO_CONNECT_TIME
Version has CURLINFO_PRETRANSFER_TIME
Version has CURLINFO_SIZE_UPLOAD
Version has CURLINFO_SIZE_DOWNLOAD
Version has CURLINFO_SPEED_DOWNLOAD
Version has CURLINFO_SPEED_UPLOAD
Version has CURLINFO_HEADER_SIZE
Version has CURLINFO_REQUEST_SIZE
Version has CURLINFO_SSL_VERIFYRESULT
Version has CURLINFO_FILETIME
Version has CURLINFO_CONTENT_LENGTH_DOWNLOAD
Version has CURLINFO_CONTENT_LENGTH_UPLOAD
Version has CURLINFO_STARTTRANSFER_TIME
Version has CURLINFO_CONTENT_TYPE
Version has CURLINFO_REDIRECT_TIME
Version has CURLINFO_REDIRECT_COUNT
Version has CURLINFO_PRIVATE
Version has CURLINFO_HTTP_CONNECTCODE
Version has CURLINFO_HTTPAUTH_AVAIL
Version has CURLINFO_PROXYAUTH_AVAIL
Version has CURLINFO_OS_ERRNO
Version has CURLINFO_NUM_CONNECTS
Version has CURLINFO_SSL_ENGINES
Version has CURLINFO_COOKIELIST
Version has CURLINFO_LASTSOCKET
Version has CURLINFO_FTP_ENTRY_PATH
Version has CURLINFO_REDIRECT_URL
Version has CURLINFO_PRIMARY_IP
Version has CURLINFO_APPCONNECT_TIME
Version has CURLINFO_CERTINFO
Version has CURLINFO_CONDITION_UNMET
Version has CURLOPT_WRITEDATA
Version has CURLOPT_KEYPASSWD
Version has CURLOPT_DIRLISTONLY
Version has CURLOPT_APPEND
Version has CURLOPT_KRBLEVEL
Version has CURLOPT_USE_SSL
Version has CURLOPT_TIMEOUT_MS
Version has CURLOPT_CONNECTTIMEOUT_MS
Version has CURLOPT_HTTP_TRANSFER_DECODING
Version has CURLOPT_HTTP_CONTENT_DECODING
Version has CURLOPT_NEW_FILE_PERMS
Version has CURLOPT_NEW_DIRECTORY_PERMS
Version has CURLOPT_POSTREDIR
Version has CURLOPT_OPENSOCKETFUNCTION
Version has CURLOPT_OPENSOCKETDATA
Version has CURLOPT_COPYPOSTFIELDS
Version has CURLOPT_PROXY_TRANSFER_MODE
Version has CURLOPT_SEEKFUNCTION
Version has CURLOPT_SEEKDATA
Version has CURLOPT_CRLFILE
Version has CURLOPT_ISSUERCERT
Version has CURLOPT_ADDRESS_SCOPE
Version has CURLOPT_CERTINFO
Version has CURLOPT_USERNAME
Version has CURLOPT_PASSWORD
Version has CURLOPT_PROXYUSERNAME
Version has CURLOPT_PROXYPASSWORD
Version has CURLOPT_SSH_HOST_PUBLIC_KEY_MD5
Version has CURLOPT_NOPROXY
Version has CURLOPT_TFTP_BLKSIZE
Version has CURLOPT_SOCKS5_GSSAPI_SERVICE
Version has CURLOPT_SOCKS5_GSSAPI_NEC
Version has CURLOPT_PROTOCOLS
Version has CURLOPT_REDIR_PROTOCOLS
Version has CURLOPT_SSH_AUTH_TYPES
Version has CURLOPT_SSH_PUBLIC_KEYFILE
Version has CURLOPT_SSH_PRIVATE_KEYFILE
Version has CURLOPT_FTP_SSL_CCC
Version has CURLOPT_COOKIELIST
Version has CURLOPT_IGNORE_CONTENT_LENGTH
Version has CURLOPT_FTP_SKIP_PASV_IP
Version has CURLOPT_FTP_FILEMETHOD
Version has CURLOPT_LOCALPORT
Version has CURLOPT_LOCALPORTRANGE
Version has CURLOPT_CONNECT_ONLY
Version has CURLOPT_CONV_FROM_NETWORK_FUNCTION
Version has CURLOPT_CONV_TO_NETWORK_FUNCTION
Version has CURLOPT_CONV_FROM_UTF8_FUNCTION
Version has CURLOPT_MAX_SEND_SPEED_LARGE
Version has CURLOPT_MAX_RECV_SPEED_LARGE
Version has CURLOPT_FTP_ALTERNATIVE_TO_USER
Version has CURLOPT_SOCKOPTFUNCTION
Version has CURLOPT_SOCKOPTDATA
Version has CURLOPT_SSL_SESSIONID_CACHE
libcurl version: libcurl 7.52.1
configure: creating ./config.status
config.status: creating src/Makevars

** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c base64.c -o base64.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c curl.c -o curl.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c curlInit.c -o curlInit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c curl_base64.c -o curl_base64.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c enums.c -o enums.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c json.c -o json.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c memoryManagement.c -o memoryManagement.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -DHAVE_LIBIDN_FIELD=1 -DHAVE_CURLOPT_URL=1 -DHAVE_CURLINFO_EFFECTIVE_URL=1 -DHAVE_CURLINFO_RESPONSE_CODE=1 -DHAVE_CURLINFO_TOTAL_TIME=1 -DHAVE_CURLINFO_NAMELOOKUP_TIME=1 -DHAVE_CURLINFO_CONNECT_TIME=1 -DHAVE_CURLINFO_PRETRANSFER_TIME=1 -DHAVE_CURLINFO_SIZE_UPLOAD=1 -DHAVE_CURLINFO_SIZE_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_DOWNLOAD=1 -DHAVE_CURLINFO_SPEED_UPLOAD=1 -DHAVE_CURLINFO_HEADER_SIZE=1 -DHAVE_CURLINFO_REQUEST_SIZE=1 -DHAVE_CURLINFO_SSL_VERIFYRESULT=1 -DHAVE_CURLINFO_FILETIME=1 -DHAVE_CURLINFO_CONTENT_LENGTH_DOWNLOAD=1 -DHAVE_CURLINFO_CONTENT_LENGTH_UPLOAD=1 -DHAVE_CURLINFO_STARTTRANSFER_TIME=1 -DHAVE_CURLINFO_CONTENT_TYPE=1 -DHAVE_CURLINFO_REDIRECT_TIME=1 -DHAVE_CURLINFO_REDIRECT_COUNT=1 -DHAVE_CURLINFO_PRIVATE=1 -DHAVE_CURLINFO_HTTP_CONNECTCODE=1 -DHAVE_CURLINFO_HTTPAUTH_AVAIL=1 -DHAVE_CURLINFO_PROXYAUTH_AVAIL=1 -DHAVE_CURLINFO_OS_ERRNO=1 -DHAVE_CURLINFO_NUM_CONNECTS=1 -DHAVE_CURLINFO_SSL_ENGINES=1 -DHAVE_CURLINFO_COOKIELIST=1 -DHAVE_CURLINFO_LASTSOCKET=1 -DHAVE_CURLINFO_FTP_ENTRY_PATH=1 -DHAVE_CURLINFO_REDIRECT_URL=1 -DHAVE_CURLINFO_PRIMARY_IP=1 -DHAVE_CURLINFO_APPCONNECT_TIME=1 -DHAVE_CURLINFO_CERTINFO=1 -DHAVE_CURLINFO_CONDITION_UNMET=1 -DHAVE_CURLOPT_WRITEDATA=1 -DHAVE_CURLOPT_KEYPASSWD=1 -DHAVE_CURLOPT_DIRLISTONLY=1 -DHAVE_CURLOPT_APPEND=1 -DHAVE_CURLOPT_KRBLEVEL=1 -DHAVE_CURLOPT_USE_SSL=1 -DHAVE_CURLOPT_TIMEOUT_MS=1 -DHAVE_CURLOPT_CONNECTTIMEOUT_MS=1 -DHAVE_CURLOPT_HTTP_TRANSFER_DECODING=1 -DHAVE_CURLOPT_HTTP_CONTENT_DECODING=1 -DHAVE_CURLOPT_NEW_FILE_PERMS=1 -DHAVE_CURLOPT_NEW_DIRECTORY_PERMS=1 -DHAVE_CURLOPT_POSTREDIR=1 -DHAVE_CURLOPT_OPENSOCKETFUNCTION=1 -DHAVE_CURLOPT_OPENSOCKETDATA=1 -DHAVE_CURLOPT_COPYPOSTFIELDS=1 -DHAVE_CURLOPT_PROXY_TRANSFER_MODE=1 -DHAVE_CURLOPT_SEEKFUNCTION=1 -DHAVE_CURLOPT_SEEKDATA=1 -DHAVE_CURLOPT_CRLFILE=1 -DHAVE_CURLOPT_ISSUERCERT=1 -DHAVE_CURLOPT_ADDRESS_SCOPE=1 -DHAVE_CURLOPT_CERTINFO=1 -DHAVE_CURLOPT_USERNAME=1 -DHAVE_CURLOPT_PASSWORD=1 -DHAVE_CURLOPT_PROXYUSERNAME=1 -DHAVE_CURLOPT_PROXYPASSWORD=1 -DHAVE_CURLOPT_SSH_HOST_PUBLIC_KEY_MD5=1 -DHAVE_CURLOPT_NOPROXY=1 -DHAVE_CURLOPT_TFTP_BLKSIZE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_SERVICE=1 -DHAVE_CURLOPT_SOCKS5_GSSAPI_NEC=1 -DHAVE_CURLOPT_PROTOCOLS=1 -DHAVE_CURLOPT_REDIR_PROTOCOLS=1 -DHAVE_CURLOPT_SSH_AUTH_TYPES=1 -DHAVE_CURLOPT_SSH_PUBLIC_KEYFILE=1 -DHAVE_CURLOPT_SSH_PRIVATE_KEYFILE=1 -DHAVE_CURLOPT_FTP_SSL_CCC=1 -DHAVE_CURLOPT_COOKIELIST=1 -DHAVE_CURLOPT_IGNORE_CONTENT_LENGTH=1 -DHAVE_CURLOPT_FTP_SKIP_PASV_IP=1 -DHAVE_CURLOPT_FTP_FILEMETHOD=1 -DHAVE_CURLOPT_LOCALPORT=1 -DHAVE_CURLOPT_LOCALPORTRANGE=1 -DHAVE_CURLOPT_CONNECT_ONLY=1 -DHAVE_CURLOPT_CONV_FROM_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_TO_NETWORK_FUNCTION=1 -DHAVE_CURLOPT_CONV_FROM_UTF8_FUNCTION=1 -DHAVE_CURLOPT_MAX_SEND_SPEED_LARGE=1 -DHAVE_CURLOPT_MAX_RECV_SPEED_LARGE=1 -DHAVE_CURLOPT_FTP_ALTERNATIVE_TO_USER=1 -DHAVE_CURLOPT_SOCKOPTFUNCTION=1 -DHAVE_CURLOPT_SOCKOPTDATA=1 -DHAVE_CURLOPT_SSL_SESSIONID_CACHE=1 -I/usr/include/libxml2  -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c myUTF8.c -o myUTF8.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RCurl.so base64.o curl.o curlInit.o curl_base64.o enums.o json.o memoryManagement.o myUTF8.o -lcurl -lxml2 -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-RCurl/00new/RCurl/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RCurl)
* installing *source* package ‘hwriter’ ...
** package ‘hwriter’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (hwriter)
* installing *source* package ‘zlibbioc’ ...
** using staged installation

configure: creating ./config.status
config.status: creating src/Makevars

** libs

mkdir -p "/usr/local/lib/R/site-library/00LOCK-zlibbioc/00new/zlibbioc/include"
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_zlibbioc.c -o R_init_zlibbioc.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o zlibbioc.so R_init_zlibbioc.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-zlibbioc/00new/zlibbioc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (zlibbioc)
* installing *source* package ‘latticeExtra’ ...
** package ‘latticeExtra’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (latticeExtra)
* installing *source* package ‘locfit’ ...
** package ‘locfit’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S_enter.c -o S_enter.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c band.c -o band.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dbinom.c -o dbinom.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dens_haz.c -o dens_haz.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dens_int.c -o dens_int.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c dens_odi.c -o dens_odi.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c density.c -o density.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_atree.c -o ev_atree.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_interp.c -o ev_interp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_kdtre.c -o ev_kdtre.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_main.c -o ev_main.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_sphere.c -o ev_sphere.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ev_trian.c -o ev_trian.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c family.c -o family.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fitted.c -o fitted.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c frend.c -o frend.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_adap.c -o lf_adap.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_dercor.c -o lf_dercor.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_fitfun.c -o lf_fitfun.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_nbhd.c -o lf_nbhd.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_robust.c -o lf_robust.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_vari.c -o lf_vari.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lf_wdiag.c -o lf_wdiag.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lfstr.c -o lfstr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c locfit.c -o locfit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_chol.c -o m_chol.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_eigen.c -o m_eigen.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_icirc.c -o m_icirc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_imont.c -o m_imont.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_isimp.c -o m_isimp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_isphr.c -o m_isphr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_jacob.c -o m_jacob.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_max.c -o m_max.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_qr.c -o m_qr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_solve.c -o m_solve.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_svd.c -o m_svd.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c m_vector.c -o m_vector.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c math.c -o math.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c minmax.c -o minmax.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pcomp.c -o pcomp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c preplot.c -o preplot.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c prob.c -o prob.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c procv.c -o procv.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scb.c -o scb.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scb_cons.c -o scb_cons.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scb_crit.c -o scb_crit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scb_iface.c -o scb_iface.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c simul.c -o simul.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c smisc.c -o smisc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c startlf.c -o startlf.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c weight.c -o weight.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o locfit.so S_enter.o band.o dbinom.o dens_haz.o dens_int.o dens_odi.o density.o ev_atree.o ev_interp.o ev_kdtre.o ev_main.o ev_sphere.o ev_trian.o family.o fitted.o frend.o lf_adap.o lf_dercor.o lf_fitfun.o lf_nbhd.o lf_robust.o lf_vari.o lf_wdiag.o lfstr.o locfit.o m_chol.o m_eigen.o m_icirc.o m_imont.o m_isimp.o m_isphr.o m_jacob.o m_max.o m_qr.o m_solve.o m_svd.o m_vector.o math.o minmax.o pcomp.o preplot.o prob.o procv.o scb.o scb_cons.o scb_crit.o scb_iface.o simul.o smisc.o startlf.o weight.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-locfit/00new/locfit/libs
** R
** data
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (locfit)
* installing *source* package ‘RcppArmadillo’ ...
** package ‘RcppArmadillo’ successfully unpacked and MD5 sums checked
** using staged installation

checking whether the C++ compiler works... yes
checking for C++ compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C++ compiler... yes
checking whether g++ -std=gnu++11 accepts -g... yes
checking how to run the C++ preprocessor... g++ -std=gnu++11 -E
checking whether we are using the GNU C++ compiler... (cached) yes
checking whether g++ -std=gnu++11 accepts -g... (cached) yes
checking whether g++ version is sufficient... yes, with OpenMP as version 6.3.0
checking for macOS... checking LAPACK_LIBS... R-supplied partial LAPACK found
checking for OpenMP... 

configure: WARNING: Some complex-valued LAPACK functions may not be available

found and suitable
configure: creating ./config.status
config.status: creating inst/include/RcppArmadilloConfigGenerated.h
config.status: creating src/Makevars

** libs

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppArmadillo.cpp -o RcppArmadillo.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I/usr/local/include -I../inst/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fastLm.cpp -o fastLm.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o RcppArmadillo.so RcppArmadillo.o RcppExports.o fastLm.o -fopenmp -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-RcppArmadillo/00new/RcppArmadillo/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (RcppArmadillo)
* installing *source* package ‘Rhtslib’ ...
** using non-staged installation via StagedInstall field
** libs

cd "htslib-1.7" && make -f "/usr/local/lib/R/etc/Makeconf" -f "Makefile.Rhtslib"
make[1]: Entering directory '/tmp/Rtmp9UBj9g/R.INSTALL109116cd6706/Rhtslib/src/htslib-1.7'

Makefile.Rhtslib:128: warning: overriding recipe for target '.c.o'
/usr/local/lib/R/etc/Makeconf:167: warning: ignoring old recipe for target '.c.o'

gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kfunc.o kfunc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o knetfile.o knetfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o kstring.o kstring.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bcf_sr_sort.o bcf_sr_sort.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o bgzf.o bgzf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o errmod.o errmod.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o faidx.o faidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile.o hfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_net.o hfile_net.c
echo '#define HTS_VERSION "1.7"' > version.h
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts.o hts.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hts_os.o hts_os.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o md5.o md5.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o multipart.o multipart.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o probaln.o probaln.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o realn.o realn.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o regidx.o regidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o sam.o sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o synced_bcf_reader.o synced_bcf_reader.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf_sweep.o vcf_sweep.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o tbx.o tbx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o textutils.o textutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o thread_pool.o thread_pool.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcf.o vcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o vcfutils.o vcfutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_codecs.o cram/cram_codecs.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_decode.o cram/cram_decode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_encode.o cram/cram_encode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_external.o cram/cram_external.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_index.o cram/cram_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_io.o cram/cram_io.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_samtools.o cram/cram_samtools.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/cram_stats.o cram/cram_stats.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/files.o cram/files.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/mFILE.o cram/mFILE.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/open_trace_file.o cram/open_trace_file.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/pooled_alloc.o cram/pooled_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/rANS_static.o cram/rANS_static.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/sam_header.o cram/sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o cram/string_alloc.o cram/string_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64 -c -o hfile_libcurl.o hfile_libcurl.c
ar -rc libhts.a kfunc.o knetfile.o kstring.o bcf_sr_sort.o bgzf.o errmod.o faidx.o hfile.o hfile_net.o hts.o hts_os.o md5.o multipart.o probaln.o realn.o regidx.o sam.o synced_bcf_reader.o vcf_sweep.o tbx.o textutils.o thread_pool.o vcf.o vcfutils.o cram/cram_codecs.o cram/cram_decode.o cram/cram_encode.o cram/cram_external.o cram/cram_index.o cram/cram_io.o cram/cram_samtools.o cram/cram_stats.o cram/files.o cram/mFILE.o cram/open_trace_file.o cram/pooled_alloc.o cram/rANS_static.o cram/sam_header.o cram/string_alloc.o hfile_libcurl.o
ranlib libhts.a
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kfunc.pico kfunc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o knetfile.pico knetfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o kstring.pico kstring.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bcf_sr_sort.pico bcf_sr_sort.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o bgzf.pico bgzf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o errmod.pico errmod.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o faidx.pico faidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile.pico hfile.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_net.pico hfile_net.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts.pico hts.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hts_os.pico hts_os.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o md5.pico md5.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o multipart.pico multipart.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o probaln.pico probaln.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o realn.pico realn.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o regidx.pico regidx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o sam.pico sam.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o synced_bcf_reader.pico synced_bcf_reader.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf_sweep.pico vcf_sweep.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o tbx.pico tbx.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o textutils.pico textutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o thread_pool.pico thread_pool.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcf.pico vcf.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o vcfutils.pico vcfutils.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_codecs.pico cram/cram_codecs.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_decode.pico cram/cram_decode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_encode.pico cram/cram_encode.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_external.pico cram/cram_external.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_index.pico cram/cram_index.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_io.pico cram/cram_io.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_samtools.pico cram/cram_samtools.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/cram_stats.pico cram/cram_stats.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/files.pico cram/files.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/mFILE.pico cram/mFILE.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/open_trace_file.pico cram/open_trace_file.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/pooled_alloc.pico cram/pooled_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/rANS_static.pico cram/rANS_static.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/sam_header.pico cram/sam_header.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o cram/string_alloc.pico cram/string_alloc.c
gcc -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -fpic -I. -I/usr/local/include -D_FILE_OFFSET_BITS=64  -c -o hfile_libcurl.pico hfile_libcurl.c
gcc -shared -Wl,-soname,libhts.so.2 -L/usr/local/lib -o libhts.so kfunc.pico knetfile.pico kstring.pico bcf_sr_sort.pico bgzf.pico errmod.pico faidx.pico hfile.pico hfile_net.pico hts.pico hts_os.pico md5.pico multipart.pico probaln.pico realn.pico regidx.pico sam.pico synced_bcf_reader.pico vcf_sweep.pico tbx.pico textutils.pico thread_pool.pico vcf.pico vcfutils.pico cram/cram_codecs.pico cram/cram_decode.pico cram/cram_encode.pico cram/cram_external.pico cram/cram_index.pico cram/cram_io.pico cram/cram_samtools.pico cram/cram_stats.pico cram/files.pico cram/mFILE.pico cram/open_trace_file.pico cram/pooled_alloc.pico cram/rANS_static.pico cram/sam_header.pico cram/string_alloc.pico hfile_libcurl.pico -lz -lm -lbz2 -llzma -lcurl -lpthread
ln -sf libhts.so libhts.so.2
make[1]: Leaving directory '/tmp/Rtmp9UBj9g/R.INSTALL109116cd6706/Rhtslib/src/htslib-1.7'
mkdir -p "/usr/local/lib/R/site-library/Rhtslib/include/htslib"
cd "htslib-1.7/htslib" && cp * "/usr/local/lib/R/site-library/Rhtslib/include/htslib" && cd .. && cp textutils_internal.h hts_internal.h "/usr/local/lib/R/site-library/Rhtslib/include"
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/zlibbioc/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rhtslib.c -o R_init_Rhtslib.o
mkdir -p "/usr/local/lib/R/site-library/Rhtslib/usrlib"
cd "htslib-1.7" && cp libhts.so libhts.a "/usr/local/lib/R/site-library/Rhtslib/usrlib"
cd "/usr/local/lib/R/site-library/Rhtslib/usrlib" && ln -s libhts.so libhts.so.2
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rhtslib.so R_init_Rhtslib.o /usr/local/lib/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/local/lib/R/lib -lR
mkdir -p "/usr/local/lib/R/site-library/Rhtslib/testdata/tabix"
cd "htslib-1.7/test" && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/usr/local/lib/R/site-library/Rhtslib/testdata" 2>/dev/null || true) && cd tabix && (cp *.sam *.bam *.vcf *.bcf *.cram *.fa *.fa.fai *.gff *.bed "/usr/local/lib/R/site-library/Rhtslib/testdata/tabix" 2>/dev/null || true)

installing to /usr/local/lib/R/site-library/Rhtslib/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (Rhtslib)
* installing *source* package ‘futile.logger’ ...
** package ‘futile.logger’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (futile.logger)
* installing *source* package ‘htmlTable’ ...
** package ‘htmlTable’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (htmlTable)
* installing *source* package ‘viridis’ ...
** package ‘viridis’ successfully unpacked and MD5 sums checked
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (viridis)
* installing *source* package ‘S4Vectors’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c AEbufs.c -o AEbufs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DataFrame_class.c -o DataFrame_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hits_class.c -o Hits_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c LLint_class.c -o LLint_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c List_class.c -o List_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_S4Vectors.c -o R_init_S4Vectors.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_class.c -o Rle_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rle_utils.c -o Rle_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SEXP_utils.c -o SEXP_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleList_class.c -o SimpleList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c character_utils.c -o character_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c eval_utils.c -o eval_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c hash_utils.c -o hash_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c integer_utils.c -o integer_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c logical_utils.c -o logical_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c map_ranges_to_runs.c -o map_ranges_to_runs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c raw_utils.c -o raw_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c safe_arithm.c -o safe_arithm.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sort_utils.c -o sort_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c subsetting_utils.c -o subsetting_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_utils.c -o vector_utils.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o S4Vectors.so AEbufs.o DataFrame_class.o Hits_class.o LLint_class.o List_class.o R_init_S4Vectors.o Rle_class.o Rle_utils.o SEXP_utils.o SimpleList_class.o anyMissing.o character_utils.o eval_utils.o hash_utils.o integer_utils.o logical_utils.o map_ranges_to_runs.o raw_utils.o safe_arithm.o sort_utils.o subsetting_utils.o vector_utils.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-S4Vectors/00new/S4Vectors/libs
** R
** inst
** byte-compile and prepare package for lazy loading

in method for ‘normalizeSingleBracketReplacementValue’ with signature ‘"List"’: no definition for class “List”
Creating a generic function for ‘complete.cases’ from package ‘stats’ in package ‘S4Vectors’
Creating a new generic function for ‘expand.grid’ in package ‘S4Vectors’
Creating a new generic function for ‘findMatches’ in package ‘S4Vectors’
Creating a generic function for ‘setequal’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘as.factor’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tabulate’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘cov’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘cor’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘S4Vectors’
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘substring’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘S4Vectors’
Creating a generic function for ‘nlevels’ from package ‘base’ in package ‘S4Vectors’
in method for ‘coerce’ with signature ‘"data.table","DFrame"’: no definition for class “data.table”

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (S4Vectors)
* installing *source* package ‘Biobase’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Rinit.c -o Rinit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c anyMissing.c -o anyMissing.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c envir.c -o envir.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchpt.c -o matchpt.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowMedians.c -o rowMedians.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sublist_extract.c -o sublist_extract.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biobase.so Rinit.o anyMissing.o envir.o matchpt.o rowMedians.o sublist_extract.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-Biobase/00new/Biobase/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biobase)
* installing *source* package ‘IRanges’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedAtomicList_utils.c -o CompressedAtomicList_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedIRangesList_class.c -o CompressedIRangesList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c CompressedList_class.c -o CompressedList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Grouping_class.c -o Grouping_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IPosRanges_comparison.c -o IPosRanges_comparison.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_class.c -o IRanges_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_constructor.c -o IRanges_constructor.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c NCList.c -o NCList.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_IRanges.c -o R_init_IRanges.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ranges_class.c -o Ranges_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RleViews_utils.c -o RleViews_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SimpleIRangesList_class.c -o SimpleIRangesList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coverage_methods.c -o coverage_methods.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c extractListFragments.c -o extractListFragments.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inter_range_methods.c -o inter_range_methods.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o IRanges.so CompressedAtomicList_utils.o CompressedIRangesList_class.o CompressedList_class.o Grouping_class.o IPosRanges_comparison.o IRanges_class.o IRanges_constructor.o NCList.o R_init_IRanges.o Ranges_class.o RleViews_utils.o S4Vectors_stubs.o SimpleIRangesList_class.o coverage_methods.o extractListFragments.o inter_range_methods.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-IRanges/00new/IRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading

Creating a generic function for ‘drop’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘runmed’ from package ‘stats’ in package ‘IRanges’
Creating a generic function for ‘chartr’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘toupper’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘tolower’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘sub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘gsub’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘startsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘endsWith’ from package ‘base’ in package ‘IRanges’
Creating a generic function for ‘smoothEnds’ from package ‘stats’ in package ‘IRanges’

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (IRanges)
* installing *source* package ‘BiocParallel’ ...
** using staged installation

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for shm_open in -lrt... yes
configure: creating ./config.status
config.status: creating src/Makevars

** libs

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/BH/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ipcmutex.cpp -o ipcmutex.o

In file included from /usr/local/lib/R/site-library/BH/include/boost/random/detail/integer_log2.hpp:19:0,
                 from /usr/local/lib/R/site-library/BH/include/boost/random/detail/large_arithmetic.hpp:19,
                 from /usr/local/lib/R/site-library/BH/include/boost/random/detail/const_mod.hpp:23,
                 from /usr/local/lib/R/site-library/BH/include/boost/random/detail/seed_impl.hpp:26,
                 from /usr/local/lib/R/site-library/BH/include/boost/random/mersenne_twister.hpp:30,
                 from /usr/local/lib/R/site-library/BH/include/boost/uuid/random_generator.hpp:17,
                 from /usr/local/lib/R/site-library/BH/include/boost/uuid/uuid_generators.hpp:17,
                 from ipcmutex.cpp:3:
/usr/local/lib/R/site-library/BH/include/boost/pending/integer_log2.hpp:7:59: note: #pragma message: This header is deprecated. Use <boost/integer/integer_log2.hpp> instead.
 BOOST_HEADER_DEPRECATED("<boost/integer/integer_log2.hpp>");
                                                           ^

g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o BiocParallel.so ipcmutex.o -lrt -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-BiocParallel/00new/BiocParallel/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (BiocParallel)
* installing *source* package ‘Hmisc’ ...
** package ‘Hmisc’ successfully unpacked and MD5 sums checked
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Hmisc.c -o Hmisc.o
gfortran  -fpic  -g -O2  -c cidxcn.f -o cidxcn.o
gfortran  -fpic  -g -O2  -c cidxcp.f -o cidxcp.o
gfortran  -fpic  -g -O2  -c hoeffd.f -o hoeffd.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gfortran  -fpic  -g -O2  -c jacklins.f -o jacklins.o
gfortran  -fpic  -g -O2  -c largrec.f -o largrec.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c mChoice.c -o mChoice.o
gfortran  -fpic  -g -O2  -c maxempr.f -o maxempr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nstr.c -o nstr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ranksort.c -o ranksort.o
gfortran  -fpic  -g -O2  -c rcorr.f -o rcorr.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c string_box.c -o string_box.o
gfortran  -fpic  -g -O2  -c wclosest.f -o wclosest.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Hmisc.so Hmisc.o cidxcn.o cidxcp.o hoeffd.o init.o jacklins.o largrec.o mChoice.o maxempr.o nstr.o ranksort.o rcorr.o string_box.o wclosest.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-Hmisc/00new/Hmisc/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Hmisc)
* installing *source* package ‘DelayedArray’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_DelayedArray.c -o R_init_DelayedArray.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c abind.c -o abind.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c compress_atomic_vector.c -o compress_atomic_vector.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o DelayedArray.so R_init_DelayedArray.o S4Vectors_stubs.o abind.o compress_atomic_vector.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-DelayedArray/00new/DelayedArray/libs
** R
** inst
** byte-compile and prepare package for lazy loading

Creating a new generic function for ‘aperm’ in package ‘DelayedArray’
Creating a generic function for ‘sweep’ from package ‘base’ in package ‘DelayedArray’
Creating a new generic function for ‘apply’ in package ‘DelayedArray’
Creating a new generic function for ‘rowsum’ in package ‘DelayedArray’
Creating a generic function for ‘dnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qnorm’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘pbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qbinom’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘ppois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qpois’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘dlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘plogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a generic function for ‘qlogis’ from package ‘stats’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘colMaxs’ in package ‘DelayedArray’
Creating a new generic function for ‘rowMins’ in package ‘DelayedArray’
Creating a new generic function for ‘colMins’ in package ‘DelayedArray’
Creating a new generic function for ‘rowRanges’ in package ‘DelayedArray’
Creating a new generic function for ‘colRanges’ in package ‘DelayedArray’

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DelayedArray)
* installing *source* package ‘GenomeInfoDb’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomeInfoDb)
* installing *source* package ‘AnnotationDbi’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading

Creating a new generic function for ‘packageName’ in package ‘AnnotationDbi’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘eapply’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘exists’ from package ‘base’ in package ‘AnnotationDbi’
Creating a generic function for ‘sample’ from package ‘base’ in package ‘AnnotationDbi’

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (AnnotationDbi)
* installing *source* package ‘XVector’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Ocopy_byteblocks.c -o Ocopy_byteblocks.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RDS_random_access.c -o RDS_random_access.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_XVector.c -o R_init_XVector.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedDouble_class.c -o SharedDouble_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedInteger_class.c -o SharedInteger_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedRaw_class.c -o SharedRaw_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SharedVector_class.c -o SharedVector_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XDouble_class.c -o XDouble_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XInteger_class.c -o XInteger_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XRawList_comparison.c -o XRawList_comparison.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XRaw_class.c -o XRaw_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVectorList_class.c -o XVectorList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_class.c -o XVector_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_utils.c -o io_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c slice_methods.c -o slice_methods.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c vector_copy.c -o vector_copy.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c view_summarization_methods.c -o view_summarization_methods.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o XVector.so IRanges_stubs.o Ocopy_byteblocks.o RDS_random_access.o R_init_XVector.o S4Vectors_stubs.o SharedDouble_class.o SharedInteger_class.o SharedRaw_class.o SharedVector_class.o XDouble_class.o XInteger_class.o XRawList_comparison.o XRaw_class.o XVectorList_class.o XVector_class.o io_utils.o slice_methods.o vector_copy.o view_summarization_methods.o -lz -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-XVector/00new/XVector/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (XVector)
* installing *source* package ‘annotate’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (annotate)
* installing *source* package ‘GenomicRanges’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_GenomicRanges.c -o R_init_GenomicRanges.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c transcript_utils.c -o transcript_utils.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GenomicRanges.so IRanges_stubs.o R_init_GenomicRanges.o S4Vectors_stubs.o transcript_utils.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-GenomicRanges/00new/GenomicRanges/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicRanges)
* installing *source* package ‘Biostrings’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BAB_class.c -o BAB_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c BitMatrix.c -o BitMatrix.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c MIndex_class.c -o MIndex_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PreprocessedTB_class.c -o PreprocessedTB_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Biostrings.c -o R_init_Biostrings.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RoSeqs_utils.c -o RoSeqs_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c SparseList_utils.c -o SparseList_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSetList_class.c -o XStringSetList_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XStringSet_class.c -o XStringSet_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XString_class.c -o XString_class.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_needwunsQS.c -o align_needwunsQS.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_pairwiseAlignment.c -o align_pairwiseAlignment.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c align_utils.c -o align_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c find_palindromes.c -o find_palindromes.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c gtestsim.c -o gtestsim.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c inject_code.c -o inject_code.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c letter_frequency.c -o letter_frequency.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c lowlevel_matching.c -o lowlevel_matching.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_PWM.c -o match_PWM.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern.c -o match_pattern.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_boyermoore.c -o match_pattern_boyermoore.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_indels.c -o match_pattern_indels.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pattern_shiftor.c -o match_pattern_shiftor.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict.c -o match_pdict.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_ACtree2.c -o match_pdict_ACtree2.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_Twobit.c -o match_pdict_Twobit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_pdict_utils.c -o match_pdict_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c match_reporting.c -o match_reporting.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c matchprobes.c -o matchprobes.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pmatchPattern.c -o pmatchPattern.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_fasta_files.c -o read_fasta_files.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_fastq_files.c -o read_fastq_files.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replaceAt.c -o replaceAt.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c replace_letter_at.c -o replace_letter_at.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c strutils.c -o strutils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c translate.c -o translate.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c unstrsplit_methods.c -o unstrsplit_methods.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xscat.c -o xscat.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Biostrings.so BAB_class.o BitMatrix.o IRanges_stubs.o MIndex_class.o PreprocessedTB_class.o R_init_Biostrings.o RoSeqs_utils.o S4Vectors_stubs.o SparseList_utils.o XStringSetList_class.o XStringSet_class.o XString_class.o XVector_stubs.o align_needwunsQS.o align_pairwiseAlignment.o align_utils.o find_palindromes.o gtestsim.o inject_code.o letter_frequency.o lowlevel_matching.o match_PWM.o match_pattern.o match_pattern_boyermoore.o match_pattern_indels.o match_pattern_shiftor.o match_pdict.o match_pdict_ACtree2.o match_pdict_Twobit.o match_pdict_utils.o match_reporting.o matchprobes.o pmatchPattern.o read_fasta_files.o read_fastq_files.o replaceAt.o replace_letter_at.o strutils.o translate.o unstrsplit_methods.o utils.o xscat.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-Biostrings/00new/Biostrings/libs
** R
** data
** inst
** byte-compile and prepare package for lazy loading

in method for ‘twoWayAlphabetFrequencyByQuality’ with signature ‘"QualityScaledXStringSet"’: no definition for class “QualityScaledXStringSet”
Creating a new generic function for ‘strsplit’ in package ‘Biostrings’
Creating a generic function for ‘ls’ from package ‘base’ in package ‘Biostrings’
Creating a new generic function for ‘offset’ in package ‘Biostrings’

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Biostrings)
* installing *source* package ‘biomaRt’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (biomaRt)
* installing *source* package ‘SummarizedExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SummarizedExperiment)
* installing *source* package ‘Rsamtools’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c COMPAT_bcf_hdr_read.c -o COMPAT_bcf_hdr_read.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PileupBuffer.cpp -o PileupBuffer.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c PosCacheColl.cpp -o PosCacheColl.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_Rsamtools.c -o R_init_Rsamtools.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ResultManager.cpp -o ResultManager.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c as_bam.c -o as_bam.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam.c -o bam.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_data.c -o bam_data.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_mate_iter.cpp -o bam_mate_iter.o

In file included from bam_mate_iter.cpp:2:0:
BamRangeIterator.h: In member function ‘virtual void BamRangeIterator::finalize_inprogress(bamFile)’:
BamRangeIterator.h:138:39: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
         bam_seek(bfile, pos, SEEK_SET);
                                       ^
In file included from BamRangeIterator.h:7:0,
                 from bam_mate_iter.cpp:2:
BamIterator.h: In constructor ‘BamIterator::BamIterator(bamFile, const bam_index_t*)’:
BamIterator.h:87:30: warning: ignoring return value of ‘int64_t bgzf_seek(BGZF*, int64_t, int)’, declared with attribute warn_unused_result [-Wunused-result]
         bam_seek(bfile, 0, 0);
                              ^

gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_plbuf.c -o bam_plbuf.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bam_sort.c -o bam_sort.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bambuffer.c -o bambuffer.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bamfile.c -o bamfile.o

bamfile.c: In function ‘bamfile_isincomplete’:
bamfile.c:168:13: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
             bgzf_seek(bfile->file->x.bam, offset, SEEK_SET);
             ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bcffile.c -o bcffile.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encode.c -o encode.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c fafile.c -o fafile.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c idxstats.c -o idxstats.o

In file included from /usr/local/lib/R/site-library/Rhtslib/include/sam.h:29:0,
                 from bamfile.h:5,
                 from idxstats.c:1:
idxstats.c: In function ‘idxstats_bamfile’:
/usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
idxstats.c:20:5: note: in expansion of macro ‘bam_seek’
     bam_seek(fp, 0, 0);
     ^~~~~~~~

gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_sam.c -o io_sam.o

In file included from /usr/local/lib/R/site-library/Rhtslib/include/sam.h:29:0,
                 from io_sam.c:2:
io_sam.c: In function ‘_scan_bam_all’:
/usr/local/lib/R/site-library/Rhtslib/include/bam.h:57:32: warning: ignoring return value of ‘bgzf_seek’, declared with attribute warn_unused_result [-Wunused-result]
 #define bam_seek(fp, pos, dir) bgzf_seek(fp, pos, dir)
                                ^~~~~~~~~~~~~~~~~~~~~~~
io_sam.c:304:5: note: in expansion of macro ‘bam_seek’
     bam_seek(bfile->file->x.bam, bfile->pos0, SEEK_SET);
     ^~~~~~~~

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pbuffer_wrapper.cpp -o pbuffer_wrapper.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileup.cpp -o pileup.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pileupbam.c -o pileupbam.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam.c -o sam.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_opts.c -o sam_opts.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sam_utils.c -o sam_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c samtools_patch.c -o samtools_patch.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c scan_bam_data.c -o scan_bam_data.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tabixfile.c -o tabixfile.o

tabixfile.c: In function ‘index_tabix’:
tabixfile.c:190:5: warning: ‘bgzf_is_bgzf’ is deprecated: Use bgzf_compression() or hts_detect_format() instead [-Wdeprecated-declarations]
     if (bgzf_is_bgzf(fn) != 1)
     ^~
In file included from tabixfile.c:3:0:
/usr/local/lib/R/site-library/Rhtslib/include/htslib/bgzf.h:243:9: note: declared here
     int bgzf_is_bgzf(const char *fn) HTS_DEPRECATED("Use bgzf_compression() or hts_detect_format() instead");
         ^~~~~~~~~~~~

gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c tagfilter.c -o tagfilter.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utilities.c -o utilities.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/Rhtslib/include" -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c zip_compression.c -o zip_compression.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o Rsamtools.so Biostrings_stubs.o COMPAT_bcf_hdr_read.o IRanges_stubs.o PileupBuffer.o PosCacheColl.o R_init_Rsamtools.o ResultManager.o S4Vectors_stubs.o XVector_stubs.o as_bam.o bam.o bam_data.o bam_mate_iter.o bam_plbuf.o bam_sort.o bambuffer.o bamfile.o bcffile.o encode.o fafile.o idxstats.o io_sam.o pbuffer_wrapper.o pileup.o pileupbam.o sam.o sam_opts.o sam_utils.o samtools_patch.o scan_bam_data.o tabixfile.o tagfilter.o utilities.o zip_compression.o /usr/local/lib/R/site-library/Rhtslib/usrlib/libhts.a -lcurl -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-Rsamtools/00new/Rsamtools/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (Rsamtools)
* installing *source* package ‘genefilter’ ...
** using staged installation
** libs

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c half_range_mode.cpp -o half_range_mode.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c init.c -o init.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c nd.c -o nd.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c pAUC.c -o pAUC.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowPAUCs.c -o rowPAUCs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG   -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c rowttests.c -o rowttests.o
gfortran  -fpic  -g -O2  -c ttest.f -o ttest.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o genefilter.so half_range_mode.o init.o nd.o pAUC.o rowPAUCs.o rowttests.o ttest.o -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-genefilter/00new/genefilter/libs
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genefilter)
* installing *source* package ‘geneplotter’ ...
** using staged installation
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (geneplotter)
* installing *source* package ‘SingleCellExperiment’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (SingleCellExperiment)
* installing *source* package ‘GenomicAlignments’ ...
** using staged installation
** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_GenomicAlignments.c -o R_init_GenomicAlignments.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c cigar_utils.c -o cigar_utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c coordinate_mapping_methods.c -o coordinate_mapping_methods.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c encodeOverlaps_methods.c -o encodeOverlaps_methods.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicAlignments)
* installing *source* package ‘DESeq2’ ...
** using staged installation
** libs

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c DESeq2.cpp -o DESeq2.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/Rcpp/include" -I"/usr/local/lib/R/site-library/RcppArmadillo/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c RcppExports.cpp -o RcppExports.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o DESeq2.so DESeq2.o RcppExports.o -L/usr/local/lib/R/lib -lRlapack -lopenblas -lgfortran -lm -lquadmath -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-DESeq2/00new/DESeq2/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (DESeq2)
* installing *source* package ‘rtracklayer’ ...
** using staged installation

checking for pkg-config... /usr/bin/pkg-config
checking pkg-config is at least version 0.9.0... yes
checking for OPENSSL... yes
configure: creating ./config.status
config.status: creating src/Makevars

** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_rtracklayer.c -o R_init_rtracklayer.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readGFF.c -o readGFF.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c bigWig.c -o bigWig.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c chain_io.c -o chain_io.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c twoBit.c -o twoBit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c handlers.c -o handlers.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c utils.c -o utils.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bPlusTree.c -o ucsc/bPlusTree.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bbiRead.c -o ucsc/bbiRead.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bbiWrite.c -o ucsc/bbiWrite.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bwgCreate.c -o ucsc/bwgCreate.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bwgQuery.c -o ucsc/bwgQuery.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/cirTree.c -o ucsc/cirTree.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/common.c -o ucsc/common.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/dnaseq.c -o ucsc/dnaseq.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/dnautil.c -o ucsc/dnautil.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/errAbort.c -o ucsc/errAbort.o

ucsc/errAbort.c: In function ‘getThreadVars’:
ucsc/errAbort.c:331:5: warning: ignoring return value of ‘write’, declared with attribute warn_unused_result [-Wunused-result]
     write(STDERR_FILENO, errMsg, strlen(errMsg));
     ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/hash.c -o ucsc/hash.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/linefile.c -o ucsc/linefile.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/localmem.c -o ucsc/localmem.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/sqlNum.c -o ucsc/sqlNum.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/zlibFace.c -o ucsc/zlibFace.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/dystring.c -o ucsc/dystring.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/hmmstats.c -o ucsc/hmmstats.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/obscure.c -o ucsc/obscure.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/pipeline.c -o ucsc/pipeline.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/rangeTree.c -o ucsc/rangeTree.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/rbTree.c -o ucsc/rbTree.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/memalloc.c -o ucsc/memalloc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/dlist.c -o ucsc/dlist.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/udc.c -o ucsc/udc.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/net.c -o ucsc/net.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/bits.c -o ucsc/bits.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/twoBit.c -o ucsc/twoBit.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/_cheapcgi.c -o ucsc/_cheapcgi.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/internet.c -o ucsc/internet.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/https.c -o ucsc/https.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/base64.c -o ucsc/base64.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/verbose.c -o ucsc/verbose.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/os.c -o ucsc/os.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/wildcmp.c -o ucsc/wildcmp.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG -DUSE_SSL -D_FILE_OFFSET_BITS=64 -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I/usr/local/include  -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c ucsc/_portimpl.c -o ucsc/_portimpl.o
gcc -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o rtracklayer.so S4Vectors_stubs.o IRanges_stubs.o XVector_stubs.o R_init_rtracklayer.o readGFF.o bigWig.o chain_io.o twoBit.o handlers.o utils.o ucsc/bPlusTree.o ucsc/bbiRead.o ucsc/bbiWrite.o ucsc/bwgCreate.o ucsc/bwgQuery.o ucsc/cirTree.o ucsc/common.o ucsc/dnaseq.o ucsc/dnautil.o ucsc/errAbort.o ucsc/hash.o ucsc/linefile.o ucsc/localmem.o ucsc/sqlNum.o ucsc/zlibFace.o ucsc/dystring.o ucsc/hmmstats.o ucsc/obscure.o ucsc/pipeline.o ucsc/rangeTree.o ucsc/rbTree.o ucsc/memalloc.o ucsc/dlist.o ucsc/udc.o ucsc/net.o ucsc/bits.o ucsc/twoBit.o ucsc/_cheapcgi.o ucsc/internet.o ucsc/https.o ucsc/base64.o ucsc/verbose.o ucsc/os.o ucsc/wildcmp.o ucsc/_portimpl.o -lz -pthread -lssl -lcrypto -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-rtracklayer/00new/rtracklayer/libs
** R
** data
** demo
** inst
** byte-compile and prepare package for lazy loading

Creating a generic function for ‘offset’ from package ‘stats’ in package ‘rtracklayer’
Creating a generic function from function ‘uri’ in package ‘rtracklayer’

** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (rtracklayer)
* installing *source* package ‘ShortRead’ ...
** using staged installation

checking for gcc... gcc
checking whether the C compiler works... yes
checking for C compiler default output file name... a.out
checking for suffix of executables... 
checking whether we are cross compiling... no
checking for suffix of object files... o
checking whether we are using the GNU C compiler... yes
checking whether gcc accepts -g... yes
checking for gcc option to accept ISO C89... none needed
checking for gzeof in -lz... yes
checking how to run the C preprocessor... gcc -E
checking for grep that handles long lines and -e... /bin/grep
checking for egrep... /bin/grep -E
checking for ANSI C header files... yes
checking for sys/types.h... yes
checking for sys/stat.h... yes
checking for stdlib.h... yes
checking for string.h... yes
checking for memory.h... yes
checking for strings.h... yes
checking for inttypes.h... yes
checking for stdint.h... yes
checking for unistd.h... yes
checking size of unsigned long... 8
configure: creating ./config.status
config.status: creating src/Makevars

** libs

gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c Biostrings_stubs.c -o Biostrings_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c IRanges_stubs.c -o IRanges_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c R_init_ShortRead.c -o R_init_ShortRead.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c S4Vectors_stubs.c -o S4Vectors_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c XVector_stubs.c -o XVector_stubs.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c alphabet.c -o alphabet.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io.c -o io.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_bowtie.c -o io_bowtie.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c io_soap.c -o io_soap.o
g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c readBfaToc.cc -o readBfaToc.o

readBfaToc.cc: In function ‘SEXPREC* readBfaToc(SEXP)’:
readBfaToc.cc:35:59: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( seq_name, sizeof(char), name_len, fp );
                                                           ^
readBfaToc.cc:36:55: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( &seq_ori_len, sizeof(int), 1, fp );
                                                       ^
readBfaToc.cc:37:51: warning: ignoring return value of ‘size_t fread(void*, size_t, size_t, FILE*)’, declared with attribute warn_unused_result [-Wunused-result]
       (void) fread( &seq_len, sizeof(int), 1, fp );
                                                   ^

g++ -std=gnu++11 -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -DPACKAGE_NAME=\"\" -DPACKAGE_TARNAME=\"\" -DPACKAGE_VERSION=\"\" -DPACKAGE_STRING=\"\" -DPACKAGE_BUGREPORT=\"\" -DPACKAGE_URL=\"\" -DHAVE_LIBZ=1 -DSTDC_HEADERS=1 -DHAVE_SYS_TYPES_H=1 -DHAVE_SYS_STAT_H=1 -DHAVE_STDLIB_H=1 -DHAVE_STRING_H=1 -DHAVE_MEMORY_H=1 -DHAVE_STRINGS_H=1 -DHAVE_INTTYPES_H=1 -DHAVE_STDINT_H=1 -DHAVE_UNISTD_H=1 -DSIZEOF_UNSIGNED_LONG=8 -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c read_maq_map.cc -o read_maq_map.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c sampler.c -o sampler.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c trim.c -o trim.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c util.c -o util.o
gcc -I"/usr/local/lib/R/include" -DNDEBUG  -I"/usr/local/lib/R/site-library/S4Vectors/include" -I"/usr/local/lib/R/site-library/IRanges/include" -I"/usr/local/lib/R/site-library/XVector/include" -I"/usr/local/lib/R/site-library/Biostrings/include" -I/usr/local/include -fopenmp -fpic  -g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g  -c xsnap.c -o xsnap.o
g++ -std=gnu++11 -shared -L/usr/local/lib/R/lib -L/usr/local/lib -o ShortRead.so Biostrings_stubs.o IRanges_stubs.o R_init_ShortRead.o S4Vectors_stubs.o XVector_stubs.o alphabet.o io.o io_bowtie.o io_soap.o readBfaToc.o read_maq_map.o sampler.o trim.o util.o xsnap.o -lz -fopenmp -L/usr/local/lib/R/lib -lR

installing to /usr/local/lib/R/site-library/00LOCK-ShortRead/00new/ShortRead/libs
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** checking absolute paths in shared objects and dynamic libraries
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (ShortRead)
* installing *source* package ‘GenomicFeatures’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (GenomicFeatures)

The downloaded source packages are in
    ‘/tmp/Rtmp9iAvbX/downloaded_packages’

Check if packages installed

library("SingleCellExperiment")

Loading required package: SummarizedExperiment
Loading required package: GenomicRanges
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ, clusterExport, clusterMap,
    parApply, parCapply, parLapply, parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames, dirname, do.call,
    duplicated, eval, evalq, Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
    Map, mapply, match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply, union, unique, unsplit,
    which, which.max, which.min

Loading required package: S4Vectors

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

    expand.grid

Loading required package: IRanges
Loading required package: GenomeInfoDb
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with 'browseVignettes()'. To cite
    Bioconductor, see 'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

library("GenomicFeatures")

Loading required package: AnnotationDbi
Registered S3 method overwritten by 'dplyr':
  method           from
  print.rowwise_df     
Registered S3 methods overwritten by 'dbplyr':
  method         from
  print.tbl_lazy     
  print.tbl_sql      

library("GenomicAlignments")

Loading required package: Biostrings
Loading required package: XVector

Attaching package: ‘Biostrings’

The following object is masked from ‘package:base’:

    strsplit

Loading required package: Rsamtools

library("ShortRead")
library("DESeq2")

Registered S3 method overwritten by 'htmlwidgets':
  method           from         
  print.htmlwidget tools:rstudio
Registered S3 method overwritten by 'data.table':
  method           from
  print.data.table     

Installed packages

rownames(installed.packages(.libPaths()[1]))

  [1] "acepack"              "annotate"             "AnnotationDbi"        "askpass"             
  [5] "assertthat"           "backports"            "base64enc"            "BH"                  
  [9] "bigrquery"            "Biobase"              "BiocFileCache"        "BiocGenerics"        
 [13] "BiocManager"          "BiocParallel"         "BiocVersion"          "biomaRt"             
 [17] "Biostrings"           "bit"                  "bit64"                "bitops"              
 [21] "blob"                 "brew"                 "broom"                "callr"               
 [25] "caTools"              "cellranger"           "checkmate"            "cli"                 
 [29] "clipr"                "clisymbols"           "colorspace"           "commonmark"          
 [33] "covr"                 "crayon"               "crosstalk"            "curl"                
 [37] "cyclocomp"            "data.table"           "DBI"                  "dbplyr"              
 [41] "DelayedArray"         "desc"                 "DESeq2"               "devtools"            
 [45] "digest"               "docopt"               "dplyr"                "DT"                  
 [49] "dtplyr"               "ellipsis"             "evaluate"             "fansi"               
 [53] "farver"               "fastmap"              "feather"              "foghorn"             
 [57] "forcats"              "formatR"              "Formula"              "fs"                  
 [61] "futile.logger"        "futile.options"       "gargle"               "genefilter"          
 [65] "geneplotter"          "generics"             "GenomeInfoDb"         "GenomeInfoDbData"    
 [69] "GenomicAlignments"    "GenomicFeatures"      "GenomicRanges"        "ggplot2"             
 [73] "gh"                   "git2r"                "glue"                 "gmailr"              
 [77] "googleAuthR"          "googleCloudStorageR"  "gridExtra"            "gtable"              
 [81] "haven"                "highlight"            "highr"                "Hmisc"               
 [85] "hms"                  "htmlTable"            "htmltools"            "htmlwidgets"         
 [89] "httpuv"               "httr"                 "hunspell"             "hwriter"             
 [93] "ini"                  "IRanges"              "jsonlite"             "knitr"               
 [97] "labeling"             "Lahman"               "lambda.r"             "later"               
[101] "latticeExtra"         "lazyeval"             "lifecycle"            "lintr"               
[105] "littler"              "locfit"               "lubridate"            "magrittr"            
[109] "markdown"             "matrixStats"          "memoise"              "microbenchmark"      
[113] "mime"                 "mockery"              "modelr"               "munsell"             
[117] "nycflights13"         "openssl"              "parsedate"            "pillar"              
[121] "pingr"                "pkgbuild"             "pkgconfig"            "pkgdown"             
[125] "pkgload"              "plogr"                "plyr"                 "praise"              
[129] "prettyunits"          "processx"             "progress"             "promises"            
[133] "ps"                   "purrr"                "R6"                   "rapidjsonr"          
[137] "rappdirs"             "rcmdcheck"            "RColorBrewer"         "Rcpp"                
[141] "RcppArmadillo"        "RCurl"                "readr"                "readxl"              
[145] "rematch"              "rematch2"             "remotes"              "reprex"              
[149] "reshape2"             "rex"                  "Rhtslib"              "rhub"                
[153] "rlang"                "rmarkdown"            "RMySQL"               "Ronaldo"             
[157] "roxygen2"             "RPostgreSQL"          "rprojroot"            "Rsamtools"           
[161] "RSQLite"              "rstudioapi"           "rtracklayer"          "rversions"           
[165] "rvest"                "S4Vectors"            "scales"               "selectr"             
[169] "sessioninfo"          "shiny"                "ShortRead"            "SingleCellExperiment"
[173] "snow"                 "sourcetools"          "spelling"             "stringdist"          
[177] "stringi"              "stringr"              "SummarizedExperiment" "sys"                 
[181] "testit"               "testthat"             "tibble"               "tidyr"               
[185] "tidyselect"           "tidyverse"            "tinytex"              "usethis"             
[189] "utf8"                 "uuid"                 "vctrs"                "viridis"             
[193] "viridisLite"          "whisker"              "whoami"               "withr"               
[197] "xfun"                 "XML"                  "xml2"                 "xmlparsedata"        
[201] "xopen"                "xtable"               "XVector"              "yaml"                
[205] "zeallot"              "zip"                  "zlibbioc"