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 28/119 | Hostname | OS / Arch | BUILD | BIOCCHECK | |||||||
biovizBase 1.53.0 (landing page) Michael Lawrence
| nebbiolo1 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | OK | ERROR | |||||||
To the developers/maintainers of the biovizBase 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: biovizBase |
Version: 1.53.0 |
Command: /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('biovizBase_1.53.0.tar.gz')" |
StartedAt: 2024-06-28 10:44:14 -0400 (Fri, 28 Jun 2024) |
EndedAt: 2024-06-28 10:45:09 -0400 (Fri, 28 Jun 2024) |
EllapsedTime: 55.3 seconds |
RetCode: None |
Status: ERROR |
Warnings: 3 |
############################################################################## ############################################################################## ### ### Running command: ### ### /home/biocbuild/bbs-3.19-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('biovizBase_1.53.0.tar.gz')" ### ############################################################################## ############################################################################## ─ BiocCheckVersion: 1.41.3 ─ BiocVersion: 3.20 ─ Package: biovizBase ─ PackageVersion: 1.53.0 ─ sourceDir: /tmp/RtmpfAP8iA/file3adbe029082aee/biovizBase ─ installDir: /tmp/RtmpfAP8iA/file3adbe050ca7686 ─ BiocCheckDir: /home/biocbuild/bbs-3.19-bioc-testing/meat/biovizBase.BiocCheck ─ platform: unix ─ isTarBall: TRUE * Installing package... * Checking for deprecated package usage... * Checking for remote package usage... * Checking for 'LazyData: true' usage... * NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed * Checking version number... * Checking for version number mismatch... * Checking version number validity... * Checking R version dependency... * NOTE: Update R version dependency from 3.5.0 to 4.4.0. * 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... Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/RtmpfAP8iA/file3adbe029082aee/biovizBase/man/CRC.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/RtmpfAP8iA/file3adbe029082aee/biovizBase/man/ideo.Rd' Warning in FUN(X[[i]], ...) : incomplete final line found on '/tmp/RtmpfAP8iA/file3adbe029082aee/biovizBase/man/ideoCyto.Rd' * 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... * 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 'URL', 'BugReports' field(s) in DESCRIPTION * Checking for Bioconductor software dependencies... Bioconductor dependencies found in Imports & Depends (64%). * 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. * Checking package installation calls in R code... * Checking for library/require of biovizBase... * WARNING: Avoid the use of 'library' or 'require' in R code * Checking coding practice... * NOTE: Avoid sapply(); use vapply() * NOTE: Avoid 1:...; use seq_len() or seq_along() * 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 * Checking parsed R code in R directory, examples, vignettes... * NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times) * Checking function lengths... * NOTE: The recommended function length is 50 lines or less. There are 15 functions greater than 50 lines. * Checking man page documentation... * WARNING: Empty or missing \format sections found in data man page(s). * 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. 12% 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; 135 lines (2%) are > 80 characters long. * NOTE: Consider 4 spaces instead of tabs; 2 lines (0%) contain tabs. * NOTE: Consider multiples of 4 spaces for line indents; 1564 lines (27%) 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. * ERROR: Add package to Watched Tags in your Support Site profile; visit https://support.bioconductor.org/accounts/edit/profile ─ BiocCheck results ── 2 ERRORS | 3 WARNINGS | 17 NOTES See the biovizBase.BiocCheck folder and run browseVignettes(package = 'BiocCheck') for details.