From 5e44c5e9b6885800eca4b8a608c0439919f2ec8c Mon Sep 17 00:00:00 2001 From: GitHub Actions Date: Sat, 1 Jan 2022 15:43:49 +0000 Subject: [PATCH] revdepcheck run - No changes to commit --- revdep/README.md | 20 +-- revdep/failures.md | 319 ++++++++++++++++----------------------------- 2 files changed, 118 insertions(+), 221 deletions(-) diff --git a/revdep/README.md b/revdep/README.md index 774fa415..95b631d4 100644 --- a/revdep/README.md +++ b/revdep/README.md @@ -10,21 +10,21 @@ |collate |C.UTF-8 | |ctype |C.UTF-8 | |tz |UTC | -|date |2021-12-14 | +|date |2022-01-01 | |pandoc |2.7.3 @ /usr/bin/pandoc | # Dependencies |package |old |new |Δ | |:--------|:-----|:-----|:--| -|openxlsx |4.2.4 |4.2.5 |* | -|Rcpp |1.0.7 |1.0.7 | | -|stringi |1.7.6 |1.7.6 | | -|zip |2.2.0 |2.2.0 | | +|openxlsx |4.2.5 |4.2.5 |NA | +|Rcpp |1.0.7 |1.0.7 |NA | +|stringi |1.7.6 |1.7.6 |NA | +|zip |2.2.0 |2.2.0 |NA | # Revdeps -## Failed to check (33) +## Failed to check (27) |package |version |error |warning |note | |:--------------|:-------|:-----|:-------|:----| @@ -32,7 +32,6 @@ |artMS |? | | | | |BoneProfileR |? | | | | |bruceR |? | | | | -|cbaf |? | | | | |CHRONOS |? | | | | |CNVPanelizer |? | | | | |CoTiMA |? | | | | @@ -47,18 +46,13 @@ |MatrixQCvis |? | | | | |MicroSEC |? | | | | |nanotatoR |? | | | | -|openPrimeR |? | | | | |parameters |? | | | | |Pigengene |? | | | | |PloGO2 |? | | | | |rbiom |? | | | | -|RIPAT |? | | | | -|sangeranalyseR |? | | | | +|sangeranalyseR |1.4.0 |1 |1 |2 | |SEtools |? | | | | -|sigFeature |? | | | | -|struct |? | | | | |structToolbox |? | | | | -|TarSeqQC |? | | | | |TPP |3.22.1 |1 | |3 | |uncoverappLib |? | | | | diff --git a/revdep/failures.md b/revdep/failures.md index 2354859c..53c12703 100644 --- a/revdep/failures.md +++ b/revdep/failures.md @@ -17,7 +17,21 @@ - +Error in download.file(url, destfile, method, mode = "wb", ...) : + download from 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz' failed +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 1472127733 != reported length 1623464748 +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 1472127733 != reported length 1623464748 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed ``` @@ -27,7 +41,21 @@ - +Error in download.file(url, destfile, method, mode = "wb", ...) : + download from 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz' failed +In addition: Warning messages: +1: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 1472127733 != reported length 1623464748 +2: In download.file(url, destfile, method, mode = "wb", ...) : + downloaded length 1472127733 != reported length 1623464748 +3: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached +4: In download.file(url, destfile, method, mode = "wb", ...) : + URL 'https://bioconductor.org/packages/3.14/data/annotation/src/contrib/MafDb.1Kgenomes.phase3.hs37d5_3.10.0.tar.gz': Timeout of 60 seconds was reached +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed +Warning in download.packages(pkgs, destdir = tmpd, available = available, : + download of package ‘MafDb.1Kgenomes.phase3.hs37d5’ failed ``` @@ -129,39 +157,6 @@ -``` -# cbaf - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - ``` # CHRONOS @@ -684,39 +679,6 @@ ERROR: lazy loading failed for package ‘hypeR’ -``` -# openPrimeR - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - ``` # parameters @@ -849,140 +811,114 @@ ERROR: lazy loading failed for package ‘hypeR’ -``` -# RIPAT - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - ``` # sangeranalyseR
-* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - -``` -# SEtools - -
+* Version: 1.4.0 +* GitHub: NA +* Source code: https://github.com/cran/sangeranalyseR +* Date/Publication: 2021-10-26 +* Number of recursive dependencies: 135 -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 +Run `revdep_details(, "sangeranalyseR")` for more info
-## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - +## In both -``` -# sigFeature +* checking whether package ‘sangeranalyseR’ can be installed ... ERROR + ``` + Installation failed. + See ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/new/sangeranalyseR.Rcheck/00install.out’ for details. + ``` -
+* checking for portable file names ... WARNING + ``` + Found the following file with a non-portable file name: + docs/wallpaperflare.com_wallpaper (1).jpg + These are not fully portable file names. + See section ‘Package structure’ in the ‘Writing R Extensions’ manual. + Found the following non-portable file paths: + sangeranalyseR/docs/build/html/_downloads/081987116457968e1b81ae1616525c7d/Sanger_contigs_unalignment.fa + sangeranalyseR/docs/build/html/_downloads/13b875bc704f73b8bd67dc07d86fc474/Sanger_contigs_alignment.fa + sangeranalyseR/docs/build/html/_downloads/144d09562ae5b2c7dc079e4bc2b33fb7/Sanger_contigs_alignment.fa + sangeranalyseR/docs/build/html/_downloads/165af37e8893cfdfa4dba91c44cd791b/Sanger_contigs_unalignment.fa + sangeranalyseR/docs/build/html/_downloads/345ac400befc4f176c75732770ec3fcb/Achl_RBNII384-13_contig.fa + ... + sangeranalyseR/docs/build/html/_downloads/a664bed9cc5d32924dc2ce60f8c60554/Sanger_all_trimmed_reads.fa + sangeranalyseR/docs/build/html/_downloads/b608796fffaaa7335a7341cffc9a9db7/Achl_ACHLO006-09_contig.fa + sangeranalyseR/docs/build/html/_downloads/b6b18aa3e34c6ae0be86c3940972dd38/Sanger_contigs_alignment.fa + sangeranalyseR/docs/build/html/_downloads/eeb554b575ee5b29ef733dafbf876c36/Achl_RBNII384-13_reads_alignment.fa + sangeranalyseR/docs/build/html/_downloads/fef71e7b2e1e49c01df301435e972047/Sanger_contigs_unalignment.fa + + Tarballs are only required to store paths of up to 100 bytes and cannot + store those of more than 256 bytes, with restrictions including to 100 + bytes for the final component. + See section ‘Package structure’ in the ‘Writing R Extensions’ manual. + ``` -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 +* checking package dependencies ... NOTE + ``` + Depends: includes the non-default packages: + 'stringr', 'ape', 'Biostrings', 'DECIPHER', 'parallel', 'reshape2', + 'phangorn', 'sangerseqR', 'gridExtra', 'shiny', 'shinydashboard', + 'shinyjs', 'data.table', 'plotly', 'DT', 'zeallot', 'excelR', + 'shinycssloaders', 'ggdendro', 'shinyWidgets', 'openxlsx', 'tools', + 'rmarkdown', 'knitr', 'seqinr', 'BiocStyle', 'logger' + Adding so many packages to the search path is excessive and importing + selectively is preferable. + ``` -
+* checking for hidden files and directories ... NOTE + ``` + Found the following hidden files and directories: + .travis.yml + docs/build/html/.buildinfo + These were most likely included in error. See section ‘Package + structure’ in the ‘Writing R Extensions’ manual. + ``` -## Error before installation +## Installation ### Devel ``` - - - - +* installing *source* package ‘sangeranalyseR’ ... +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘phangorn’ in dyn.load(file, DLLpath = DLLpath, ...): + unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/sangeranalyseR/igraph/libs/igraph.so': + libglpk.so.40: cannot open shared object file: No such file or directory +Execution halted +ERROR: lazy loading failed for package ‘sangeranalyseR’ +* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/new/sangeranalyseR.Rcheck/sangeranalyseR’ ``` ### CRAN ``` - - - - +* installing *source* package ‘sangeranalyseR’ ... +** using staged installation +** R +** data +** inst +** byte-compile and prepare package for lazy loading +Error: package or namespace load failed for ‘phangorn’ in dyn.load(file, DLLpath = DLLpath, ...): + unable to load shared object '/home/runner/work/openxlsx/openxlsx/revdep/library/sangeranalyseR/igraph/libs/igraph.so': + libglpk.so.40: cannot open shared object file: No such file or directory +Execution halted +ERROR: lazy loading failed for package ‘sangeranalyseR’ +* removing ‘/home/runner/work/openxlsx/openxlsx/revdep/checks/sangeranalyseR/old/sangeranalyseR.Rcheck/sangeranalyseR’ ``` -# struct +# SEtools
@@ -1047,39 +983,6 @@ ERROR: lazy loading failed for package ‘hypeR’ -``` -# TarSeqQC - -
- -* Version: -* GitHub: https://github.com/ycphs/openxlsx -* Source code: NA -* Number of recursive dependencies: 0 - -
- -## Error before installation - -### Devel - -``` - - - - - - -``` -### CRAN - -``` - - - - - - ``` # TPP