BIOCCHECK results for TMSig on nebbiolo2
To the developers/maintainers of the TMSig package:
- Allow up to 24 hours (and sometimes 48 hours) for your latest push to git@git.bioconductor.org:packages/TMSig.git to reflect on this report. See Troubleshooting Build Report for more information.
- 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.
|
raw results
Summary
Command output
##############################################################################
##############################################################################
###
### Running command:
###
### /home/biocbuild/bbs-3.24-bioc/R/bin/Rscript -e "BiocCheck::BiocCheck('TMSig_1.7.0.tar.gz','quit-with-status'=TRUE)"
###
##############################################################################
##############################################################################
── Installing TMSig ────────────────────────────────────────────────────────────
✔ Package installed successfully
── TMSig session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpu9sCfG/file14da9c30c6f277/TMSig
→ BiocVersion: 3.24
→ Package: TMSig
→ PackageVersion: 1.7.0
→ BiocCheckDir: /home/biocbuild/bbs-3.24-bioc/meat/TMSig.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/Rtmpu9sCfG/file14da9c30c6f277/TMSig
→ installDir: /tmp/Rtmpu9sCfG/file14da9c4a43b28e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on TMSig ──────────────────────────────────────────────────
* 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...
ℹ NOTE: Update R version dependency from 4.4.0 to 4.6.0
* 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...
ℹ NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, Transcription, Sequencing, ATACSeq, Microarray, Metabolomics,
Proteomics, Epigenetics, Cheminformatics, Transcriptomics,
DifferentialExpression, ExperimentalDesign, Normalization, Preprocessing,
Bayesian, Regression, ExonArray, RNASeq, OneChannel, TwoChannel, MicroRNAArray,
mRNAMicroarray, ProprietaryPlatforms, CellBiology, BiomedicalInformatics,
FunctionalGenomics, SystemsBiology, ImmunoOncology, AlternativeSplicing,
DifferentialSplicing, BatchEffect, MultipleComparison, QualityControl,
TimeCourse, DataImport
ℹ Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
ℹ Bioconductor dependencies found in Imports & Depends (27%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
ℹ NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* Checking NAMESPACE...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
ℹ NOTE: Vignette(s) found with missing chunk labels
Found in files:
• TMSig.Rmd
* Checking package installation calls in R code...
* Checking for library/require of TMSig...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
ℹ NOTE: The recommended function length is 50 lines or less. There are 4
functions greater than 50 lines.
The longest 5 functions are:
• cameraPR.matrix() (R/cameraPR.matrix.R): 202 lines
• ...
• .enrichmap_prepare_x() (R/utils.R): 68 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
ℹ NOTE: Consider multiples of 4 spaces for line indents; 257 lines (10%) are
not.
First few lines:
• R/cameraPR.matrix.R#L171 "at least 3 nonmissing valu ...
• ...
• vignettes/TMSig.Rmd#L579 )) ...
ℹ See https://contributions.bioconductor.org/r-code.html
ℹ 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...
ℹ 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...
ℹ Maintainer is registered at support site.
ℹ Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | ℹ 7 NOTES
ℹ See the TMSig.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.
