| Back to BiocCheck report for a small subset of BioC 3.18 packages |
This page was generated on 2023-10-24 11:15:02 -0400 (Tue, 24 Oct 2023).
| Hostname | OS | Arch (*) | R version | Installed pkgs |
|---|---|---|---|---|
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) | x86_64 | 4.3.1 (2023-06-16) -- "Beagle Scouts" | 4818 |
| 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 70/92 | Hostname | OS / Arch | BIOCCHECK | |||||||
| rhdf5 2.47.0 (landing page) Mike Smith
| nebbiolo2 | Linux (Ubuntu 22.04.2 LTS) / x86_64 | ERROR | |||||||
|
To the developers/maintainers of the rhdf5 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: rhdf5 |
| Version: 2.47.0 |
| Command: /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rhdf5_2.47.0.tar.gz')" |
| StartedAt: 2023-10-24 10:47:53 -0400 (Tue, 24 Oct 2023) |
| EndedAt: 2023-10-24 10:48:34 -0400 (Tue, 24 Oct 2023) |
| EllapsedTime: 40.5 seconds |
| RetCode: None |
| Status: ERROR |
| Warnings: 4 |
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### Running command:
###
### /home/biocbuild/bbs-3.18-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('rhdf5_2.47.0.tar.gz')"
###
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─ BiocCheckVersion: 1.39.0
─ BiocVersion: 3.18
─ Package: rhdf5
─ PackageVersion: 2.47.0
─ sourceDir: /tmp/RtmpLFEvAg/file38e9a82fe90e75/rhdf5
─ installDir: /tmp/RtmpLFEvAg/file38e9a8a49d6ac
─ BiocCheckDir: /home/biocbuild/bbs-3.18-bioc-testing/meat/rhdf5.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...
* NOTE: Update R version dependency from 4.0.0 to 4.3.0.
* 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...
* 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 recommeded fields in DESCRIPTION...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* WARNING: Import S4Vectors in NAMESPACE as well as DESCRIPTION.
* WARNING: Import utils in DESCRIPTION as well as NAMESPACE.
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
* Checking package installation calls in R code...
* Checking for library/require of rhdf5...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 6 times)
* ERROR: Avoid 'Sys.setenv' (found 1 times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 11 functions greater than 50 lines.
* Checking man page documentation...
* WARNING: Empty or missing \value sections found in man pages.
* 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. 4% 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; 588 lines (5%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 1691 lines
(14%) 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...
* ERROR: Maintainer must register at the support site; visit
https://support.bioconductor.org/accounts/signup/
─ BiocCheck results ──
3 ERRORS | 4 WARNINGS | 11 NOTES
See the rhdf5.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.