Back to BiocCheck report for a small subset of BioC 3.19 packages |
This page was generated on 2024-06-28 11:15:02 -0400 (Fri, 28 Jun 2024).
Hostname | OS | Arch (*) | R version | Installed pkgs |
---|---|---|---|---|
nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.4.0 (2024-04-24) -- "Puppy Cup" | 4760 |
Click on any hostname to see more info about the system (e.g. compilers) (*) as reported by 'uname -p', except on Windows and Mac OS X |
Package 81/119 | Hostname | OS / Arch | BUILD | BIOCCHECK | |||||||
pcaMethods 1.97.0 (landing page) Henning Redestig
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | ERROR | |||||||
To the developers/maintainers of the pcaMethods package: - Use the following Renviron settings to reproduce errors and warnings. - If 'R CMD check' started to fail recently on the Linux builder(s) over a missing dependency, add the missing dependency to 'Suggests:' in your DESCRIPTION file. See Renviron.bioc for more information. |
Package: pcaMethods |
Version: 1.97.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pcaMethods_1.97.0.tar.gz')" |
StartedAt: 2024-06-28 10:45:57 -0400 (Fri, 28 Jun 2024) |
EndedAt: 2024-06-28 10:46:29 -0400 (Fri, 28 Jun 2024) |
EllapsedTime: 32.3 seconds |
RetCode: None |
Status: ERROR |
Warnings: 6 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('pcaMethods_1.97.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: pcaMethods ─ PackageVersion: 1.97.0 ─ sourceDir: /tmp/RtmpqBwffi/file3b22b36eb223ef/pcaMethods ─ installDir: /tmp/RtmpqBwffi/file3b22b360b5e46e ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/pcaMethods.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R version dependency... * Checking package size... * Checking individual file sizes... * Checking biocViews... * Checking that biocViews are present... * Checking package type based on biocViews... Software * Checking for non-trivial biocViews... * Checking that biocViews come from the same category... * Checking biocViews validity... * Checking for recommended biocViews... * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (40%). * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes. * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * NOTE: 'sessionInfo' not found in vignette(s) * Checking package installation calls in R code... * Checking for library/require of pcaMethods... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 1:...; use seq_len() or seq_along() * ERROR: Use double colon for qualified imports: 'pkg::foo()' * NOTE: Avoid 'cat' and 'print' outside of 'show' methods * NOTE: Avoid using '=' for assignment and use '<-' instead * NOTE: Avoid the use of 'paste' in condition signals * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * WARNING: Avoid T/F variables; If logical, use TRUE/FALSE * WARNING: Remove set.seed usage (found 2 times) * Checking parsed R code in R directory, examples, vignettes... Found @ in man/pca.Rd * NOTE: Use accessors; don't access S4 class slots via '@' in examples/vignettes. * NOTE: Avoid '<<-' if possible (found 1 times) * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 20 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \format sections found in data man page(s). * WARNING: Empty or missing \value sections found in man page(s). * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. * Checking package NEWS... * NOTE: Consider adding a NEWS file, so your package news will be included in Bioconductor release announcements. * Checking unit tests... * NOTE: Consider adding unit tests. We strongly encourage them. See https://contributions.bioconductor.org/tests.html * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 115 lines (2%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 9 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 1439 lines (26%) are not. See https://contributions.bioconductor.org/r-code.html See styler package: https://cran.r-project.org/package=styler as described in the BiocCheck vignette. * Checking if package already exists in CRAN... * Checking for bioc-devel mailing list subscription... * NOTE: Cannot determine whether maintainer is subscribed to the Bioc-Devel mailing list (requires admin credentials). Subscribe here: https://stat.ethz.ch/mailman/listinfo/bioc-devel * Checking for support site registration... Maintainer is registered at support site. Package is in the Support Site Watched Tags. ─ BiocCheck results ── 2 ERRORS | 6 WARNINGS | 17 NOTES See the pcaMethods.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.