===============================
BiocCheckGitClone('limpa')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/4e4d6c484804d4396aadb5a4fc868ea1a7166c8f/limpa
→ BiocVersion: 3.21
→ Package: limpa
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/4e4d6c484804d4396aadb5a4fc868ea1a7166c8f/limpa.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/4e4d6c484804d4396aadb5a4fc868ea1a7166c8f/limpa
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3698/4e4d6c484804d4396aadb5a4fc868ea1a7166c8f/limpa.Rcheck’
* using R Under development (unstable) (2025-01-20 r87609)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0
* running under: Ubuntu 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘limpa/DESCRIPTION’ ... OK
* this is package ‘limpa’ version ‘0.99.4’
* checking package namespace information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘limpa’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [6s/6s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [2s/2s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘limpa-Tests.R’ [1s/1s]
Comparing ‘limpa-Tests.Rout’ to ‘limpa-Tests.Rout.save’ ... OK
[1s/1s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes ... OK
* checking running R code from vignettes ... SKIPPED
* checking re-building of vignette outputs ... SKIPPED
* checking PDF version of manual ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('limpa_0.99.4.tar.gz')
===============================
── Installing limpa ────────────────────────────────────────────────────────────
✔ Package installed successfully
── limpa session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp02MqU9/file3cd4a910166372/limpa
→ BiocVersion: 3.21
→ Package: limpa
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/4e4d6c484804d4396aadb5a4fc868ea1a7166c8f/limpa.BiocCheck
→ BiocCheckVersion: 1.43.4
→ sourceDir: /tmp/Rtmp02MqU9/file3cd4a910166372/limpa
→ installDir: /tmp/Rtmp02MqU9/file3cd4a92de1636d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on limpa ──────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* 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...
Warning in FUN(X[[i]], ...) :
incomplete final line found on '/tmp/Rtmp02MqU9/file3cd4a910166372/limpa/man/plotProtein.Rd'
i NOTE: Consider adding these automatically suggested biocViews: Transcription,
Sequencing, Microarray, Metabolomics, Epigenetics, Cheminformatics,
Transcriptomics, Normalization, Clustering, ExonArray, RNASeq, OneChannel,
TwoChannel, MicroRNAArray, mRNAMicroarray, ProprietaryPlatforms, CellBiology,
BiomedicalInformatics, FunctionalGenomics, SystemsBiology, ImmunoOncology,
AlternativeSplicing, DifferentialSplicing, GeneSetEnrichment, BatchEffect,
MultipleComparison, QualityControl, TimeCourse
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 that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of limpa...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• voomaLmFitWithImputation.R (line 72, column 32)
• voomaLmFitWithImputation.R (line 187, column 40)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/dpcDE.R (line 5, column 44)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 4 times)
• suppressWarnings() in R/peptides2ProteinBFGS.R (line 43, column 13)
• ...
• suppressWarnings() in R/voomaLmFitWithImputation.R (line 242, column 31)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
The longest 5 functions are:
• voomaLmFitWithImputation() (R/voomaLmFitWithImputation.R): 283 lines
• ...
• .estimateMuSigmaForOnePeptide() (R/dpcCN.R): 90 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• dpcquantHyperparam.Rd
• ...
• readSpectronaut.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• readDIANN.Rd
• readSpectronaut.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• readDIANN.Rd
• readSpectronaut.Rd
* 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 shorter lines; 402 lines (11%) are > 80 characters long.
First few lines:
• R/completeMomentsON.R#L13 sigma2.obs <- drop((plogis(dpc[1] + dp ...
• ...
• vignettes/limpa.Rmd#L182 The limpa project was supported by Chan ...
i NOTE: Consider 4 spaces instead of tabs; 273 lines (7%) contain tabs.
First few lines:
• R/plotProtein.R#L5 # Check input ...
• ...
• R/voomaLmFitWithImputation.R#L282 fit ...
i NOTE: Consider multiples of 4 spaces for line indents; 1137 lines (30%) are
not.
First few lines:
• R/completeMomentsON.R#L5 n <- max(length(mean.comp),length(sd.c ...
• ...
• vignettes/limpa.Rmd#L28 comment = NA ...
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 if new package already exists in Bioconductor...
* Checking for bioc-devel mailing list subscription...
i Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.43.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 12 NOTES
i See the limpa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.