Loading packages

library(BiocPkgTools)
library(BiocPkgStats)
library(newsfeed)

Packages associated with maintainer

mainpkgs <- biocMaintained(main = "marcel.ramos@roswellpark.org")
mainpkgs
## # A tibble: 14 × 47
##    Package        Version Depends Suggests License MD5sum NeedsCompilation Title
##    <chr>          <chr>   <list>  <list>   <chr>   <chr>  <chr>            <chr>
##  1 AnVIL          1.13.5  <chr>   <chr>    Artist… 6cfe5… no               "Bio…
##  2 AnVILPublish   1.11.2  <chr>   <chr>    Artist… dd340… no               "Pub…
##  3 BiocBaseUtils  1.3.0   <chr>   <chr>    Artist… 0a75e… no               "Gen…
##  4 BiocCheck      1.37.6  <chr>   <chr>    Artist… 6ecc8… no               "Bio…
##  5 BiocHubsShiny  1.1.0   <chr>   <chr>    Artist… 56782… no               "Vie…
##  6 BiocIO         1.11.0  <chr>   <chr>    Artist… 152de… no               "Sta…
##  7 cBioPortalData 2.13.6  <chr>   <chr>    AGPL-3  c6862… no               "Exp…
##  8 MultiAssayExp… 1.27.0  <chr>   <chr>    Artist… 6f05a… no               "Sof…
##  9 RaggedExperim… 1.25.1  <chr>   <chr>    Artist… 0fdf8… no               "Rep…
## 10 RTCGAToolbox   2.31.1  <chr>   <chr>    GPL-2   23b89… no               "A n…
## 11 TCGAutils      1.21.4  <chr>   <chr>    Artist… d0eb1… no               "TCG…
## 12 TENxIO         1.3.0   <chr>   <chr>    Artist… d53c0… no               "Imp…
## 13 terraTCGAdata  1.5.2   <chr>   <chr>    Artist… 75bac… no               "Ope…
## 14 UniProt.ws     2.41.4  <chr>   <chr>    Artist… 91e54… no               "R I…
## # ℹ 39 more variables: Description <chr>, biocViews <list>, Author <list>,
## #   Maintainer <list>, git_url <chr>, git_branch <chr>, git_last_commit <chr>,
## #   git_last_commit_date <chr>, `Date/Publication` <chr>, source.ver <chr>,
## #   win.binary.ver <chr>, `mac.binary.big-sur-x86_64.ver` <chr>,
## #   `mac.binary.big-sur-arm64.ver` <chr>, vignettes <list>,
## #   vignetteTitles <list>, hasREADME <chr>, hasNEWS <chr>, hasINSTALL <chr>,
## #   hasLICENSE <chr>, Rfiles <list>, dependencyCount <chr>, Imports <list>, …

Summary statistics of packages

activepkgs <- mainpkgs[["Package"]][-1:-2]
ghorgs <- c(
    rep("bioconductor", 4), rep("waldronlab", 2), "bioconductor",
    "mksamur", rep("waldronlab", 3), "bioconductor"
)

if (!file.exists("~/dlrank.Rda")) {
    restab <- generateTable(
        packages = activepkgs,
        gh_org = ghorgs,
        since_date = "2022-07-01"
    )
    save(restab, file = "~/dlrank.Rda")
} else {
    load("~/dlrank.Rda")
}

restab
##                      download.rank avg.downloads med.downloads num.revdeps
## BiocIO                           2         14183         14042           9
## MultiAssayExperiment             4          2714          2539          65
## BiocBaseUtils                    6          1673          1728           7
## BiocCheck                        7          1526          1606          10
## RaggedExperiment                10           761           747          13
## TCGAutils                       11           632           640           7
## RTCGAToolbox                    12           504           509           3
## cBioPortalData                  14           300           293           2
## UniProt.ws                      16           276           285           4
## terraTCGAdata                  101            26            32           0
## TENxIO                         103            28            25           0
## BiocHubsShiny                  104           NaN            NA           0
##                      issues.since commits.since since.date
## BiocIO                          1            12 2022-07-01
## MultiAssayExperiment           10            69 2022-07-01
## BiocBaseUtils                   0            14 2022-07-01
## BiocCheck                      38           142 2022-07-01
## RaggedExperiment                1            43 2022-07-01
## TCGAutils                       1            32 2022-07-01
## RTCGAToolbox                    3            39 2022-07-01
## cBioPortalData                  9            92 2022-07-01
## UniProt.ws                      6            77 2022-07-01
## terraTCGAdata                   0            33 2022-07-01
## TENxIO                          1           127 2022-07-01
## BiocHubsShiny                   1            36 2022-07-01

Summary of NEWS

basedirs <- ifelse(ghorgs == "bioconductor", "bioc", "gh")
pkgdirs <- paste0("~/", basedirs, "/", activepkgs)
cat(
    suppressMessages({
        collect(packages = pkgdirs)
    }),
    sep = "\n"
)

BiocBaseUtils

Changes in version 1.4.0

New features

  • Added isScalarLogical for completeness; identical to isTRUEorFALSE.

BiocCheck

CHANGES IN VERSION 1.38.0

BUG FIXES AND MINOR IMPROVEMENTS

o Improve the `read.dcf` operation that looks for any deprecated packages
in both Bioconductor release and devel versions.
o Remove overwrite prompt when updating cached resources in deprecated
packages check.

BiocHubsShiny

Changes in version 1.2.0

Bug fixes and minor improvements

  • Updated the NEWS.md file formatting

cBioPortalData

Changes in version 2.14.0

Bug fixes and minor improvements

  • Remove error when studyId build success is unknown (@vlaufer, #69)
  • Parse tokens with different formats, e.g. genie token (@ZWael, #70)

RaggedExperiment

Changes in version 1.26.0

New features

  • Added a contributed vignette for ASCAT workflows (@Lydia-King, #28).

RTCGAToolbox

Changes in version 2.32.0

New features

  • The functions getCNGECorrelation, getDiffExpressedGenes, and getSurvival have been removed from the package.

terraTCGAdata

Changes in version 1.6.0

New features

  • findTCGAworkspaces has been removed from the package.

UniProt.ws

CHANGES IN VERSION 2.42.0

NEW FEATURES

o `pageSize` and `n` arguments added to `queryUniProt` to expose
underlying API request defaults. It is recommended to set the pageSize
to a large value e.g. 500 for large queries.

BUG FIXES AND MINOR IMPROVEMENTS

o Fixed issue with pagination with large queries (over 25 results) in
`queryUniProt` (\@jdreyf, #23)

Git Logs since 2022-07-01

lapply(
    setNames(pkgdirs, nm = basename(pkgdirs)),
    function(x) {
        setwd(x)
        resp <- gert::git_log(after = "2022-07-01")[["message"]]
        resp[-grep("version bump|^bump", resp)]
    }
)

Google Doc of Bullet Points