From b7d592a94228c25417ada15fae6f2d4fe2cfc437 Mon Sep 17 00:00:00 2001 From: Tim Date: Mon, 11 Mar 2024 15:46:24 -0400 Subject: [PATCH] run revdepcheck prior to submissioin --- revdep/.gitignore | 7 ++++ revdep/.gitignore.md | 0 revdep/README.md | 30 ++++++++++++++++ revdep/cran.md | 7 ++++ revdep/failures.md | 85 ++++++++++++++++++++++++++++++++++++++++++++ revdep/problems.md | 1 + 6 files changed, 130 insertions(+) create mode 100644 revdep/.gitignore create mode 100644 revdep/.gitignore.md create mode 100644 revdep/README.md create mode 100644 revdep/cran.md create mode 100644 revdep/failures.md create mode 100644 revdep/problems.md diff --git a/revdep/.gitignore b/revdep/.gitignore new file mode 100644 index 0000000..111ab32 --- /dev/null +++ b/revdep/.gitignore @@ -0,0 +1,7 @@ +checks +library +checks.noindex +library.noindex +cloud.noindex +data.sqlite +*.html diff --git a/revdep/.gitignore.md b/revdep/.gitignore.md new file mode 100644 index 0000000..e69de29 diff --git a/revdep/README.md b/revdep/README.md new file mode 100644 index 0000000..616a278 --- /dev/null +++ b/revdep/README.md @@ -0,0 +1,30 @@ +# Platform + +|field |value | +|:--------|:-----------------------------------| +|version |R version 4.3.2 (2023-10-31) | +|os |macOS Sonoma 14.3.1 | +|system |x86_64, darwin20 | +|ui |RStudio | +|language |(EN) | +|collate |en_US.UTF-8 | +|ctype |en_US.UTF-8 | +|tz |America/New_York | +|date |2024-03-11 | +|rstudio |2023.12.1+402 Ocean Storm (desktop) | +|pandoc |2.8.0.1 @ /usr/local/bin/pandoc | + +# Dependencies + +|package |old |new |Δ | +|:-------|:-----|:----------|:--| +|LDlinkR |1.3.0 |1.3.0.9002 |* | + +# Revdeps + +## Failed to check (1) + +|package |version |error |warning |note | +|:-------|:-------|:-----|:-------|:----| +|GRaNIE |? | | | | + diff --git a/revdep/cran.md b/revdep/cran.md new file mode 100644 index 0000000..4b1b8a1 --- /dev/null +++ b/revdep/cran.md @@ -0,0 +1,7 @@ +## revdepcheck results + +We checked 2 reverse dependencies (1 from CRAN + 1 from Bioconductor), comparing R CMD check results across CRAN and dev versions of this package. + + * We saw 0 new problems + * We failed to check 0 packages + diff --git a/revdep/failures.md b/revdep/failures.md new file mode 100644 index 0000000..2af342e --- /dev/null +++ b/revdep/failures.md @@ -0,0 +1,85 @@ +# GRaNIE + +
+ +* Version: +* GitHub: https://github.com/CBIIT/LDlinkR +* Source code: NA +* Number of recursive dependencies: 0 + +
+ +## Error before installation + +### Devel + +``` + + There are binary versions available but the source versions are later: + binary source needs_compilation +digest 0.6.34 0.6.35 TRUE +tidyselect 1.2.0 1.2.1 TRUE + + Binaries will be installed + + +Error in download.file(url, destfile, method, mode = "wb", ...) : + cannot open URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz' +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +2: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘abind’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : +... +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 0 != reported length 0 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed + + +``` +### CRAN + +``` + + There are binary versions available but the source versions are later: + binary source needs_compilation +digest 0.6.34 0.6.35 TRUE +tidyselect 1.2.0 1.2.1 TRUE + + Binaries will be installed + + +Error in download.file(url, destfile, method, mode = "wb", ...) : + cannot open URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz' +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +2: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://cloud.r-project.org/bin/macosx/big-sur-x86_64/contrib/4.3/abind_1.4-5.tgz': status was 'SSL connect error' +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘abind’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : +... +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 0 != reported length 0 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.18/data/annotation/src/contrib/BSgenome.Rnorvegicus.UCSC.rn7_1.4.3.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘BSgenome.Rnorvegicus.UCSC.rn7’ failed + + +``` diff --git a/revdep/problems.md b/revdep/problems.md new file mode 100644 index 0000000..9a20736 --- /dev/null +++ b/revdep/problems.md @@ -0,0 +1 @@ +*Wow, no problems at all. :)* \ No newline at end of file