Back to BiocCheck report for a small subset of BioC 3.19 packages |
This page was generated on 2024-05-22 11:15:02 -0400 (Wed, 22 May 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" | 4751 |
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 111/119 | Hostname | OS / Arch | BUILD | BIOCCHECK | |||||||
tximeta 1.23.1 (landing page) Michael Love
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | ERROR | |||||||
To the developers/maintainers of the tximeta 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: tximeta |
Version: 1.23.1 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tximeta_1.23.1.tar.gz')" |
StartedAt: 2024-05-22 10:51:07 -0400 (Wed, 22 May 2024) |
EndedAt: 2024-05-22 10:51:59 -0400 (Wed, 22 May 2024) |
EllapsedTime: 52.9 seconds |
RetCode: None |
Status: ERROR |
Warnings: 1 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('tximeta_1.23.1.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.0 ─ BiocVersion: 3.20 ─ Package: tximeta ─ PackageVersion: 1.23.1 ─ sourceDir: /tmp/Rtmp8oHnwU/file364a674e312275/tximeta ─ installDir: /tmp/Rtmp8oHnwU/file364a67784c0401 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/tximeta.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... * WARNING: Use biocViews from one category only (one of Software, ExperimentData, AnnotationData, Workflow) Search 'biocViews' at https://contributions.bioconductor.org * Checking build system compatibility... * Checking for blank lines in DESCRIPTION... * Checking if DESCRIPTION is well formatted... * Checking for proper Description: field... * NOTE: The Description field in the DESCRIPTION is made up of less than 3 sentences. Provide a more detailed description of the package. * Checking for whitespace in DESCRIPTION field names... * Checking that Package field matches directory/tarball name... * Checking for Version: field... * Checking for valid maintainer... * NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with 'comment=c(ORCID="...")' * Checking License: for restrictive use... * Checking for recommended DESCRIPTION fields... * NOTE: Provide 'BugReports' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (68%). * Checking for pinned package versions in DESCRIPTION... * Checking .Rbuildignore... * Checking for stray BiocCheck output folders... * Checking vignette directory... * Checking package installation calls in R code... * Checking for library/require of tximeta... * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid the use of 'paste' in condition signals * NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 9 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 7 functions greater than 50 lines. * Checking man page documentation... * ERROR: At least 80% of man pages documenting exported objects must have runnable examples. * NOTE: Usage of dontrun{} / donttest{} tags found in man page examples. 8% of man pages use at least one of these tags. * NOTE: Use donttest{} instead of dontrun{}. * Checking package NEWS... * Checking unit tests... * Checking skip_on_bioc() in tests... * Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and vignette source... * NOTE: Consider shorter lines; 93 lines (3%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 1 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 747 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 ── 1 ERRORS | 1 WARNINGS | 14 NOTES See the tximeta.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.