===============================
BiocCheckGitClone('limpa')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/limpa_20250114145353/limpa
BiocVersion: 3.21
Package: limpa
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/limpa_20250114145353/limpa.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/limpa_20250114145353/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 v1.43.2 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/limpa_20250114145353/limpa.Rcheck
* using R Under development (unstable) (2024-10-21 r87258)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option --no-vignettes
* checking for file limpa/DESCRIPTION ... OK
* this is package limpa version 0.99.3
* 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 ... NOTE
Rd file 'dpcQuant.Rd':
\usage lines wider than 90 characters:
dpcQuant(y, protein.id = "Protein.Group", dpc = NULL, dpc.slope = 0.8, verbose = TRUE, ...)
Rd file 'dpcquantHyperparam.Rd':
\usage lines wider than 90 characters:
dpcQuantHyperparam(y, protein.id, dpc.slope = 0.7, sd.quantile.for.logFC = 0.9, robust = FALSE, ...)
Rd file 'fitZTLogit.Rd':
\usage lines wider than 90 characters:
fitZTLogit(n.successes, n.trials, X = NULL, capped = FALSE, beta.start = NULL, alpha.start = 0.95)
Rd file 'simProteinDataSet.Rd':
\usage lines wider than 90 characters:
simProteinDataSet(n.peptides = 100, n.groups = 2, samples.per.group = 5, peptides.per.protein = 4,
These lines will be truncated in the PDF manual.
* 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/3s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3698/limpa_20250114145353/limpa.Rcheck/00check.log
for details.
===============================
BiocCheck('limpa_0.99.3.tar.gz')
===============================
Installing limpa
Package installed successfully
limpa session metadata
sourceDir: /tmp/RtmpoM1XqS/filef2ed35298792c/limpa
BiocVersion: 3.21
Package: limpa
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3698/limpa_20250114145353/limpa.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpoM1XqS/filef2ed35298792c/limpa
installDir: /tmp/RtmpoM1XqS/filef2ed35059b76
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...
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. 9% 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; 380 lines (10%) are > 80 characters long.
First few lines:
R/completeMomentsON.R#L13 sigma2.obs <- drop((plogis(dpc[1] + dp ...
...
vignettes/limpa.Rmd#L156 The limpa project was supported by Chan ...
i NOTE: Consider 4 spaces instead of tabs; 272 lines (7%) contain tabs.
First few lines:
R/voomaLmFitWithImputation.R#L2 y, design=NULL, prior.weights=NULL, imp ...
...
R/voomaLmFitWithImputation.R#L282 fit ...
i NOTE: Consider multiples of 4 spaces for line indents; 1111 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 v1.43.2 results
0 ERRORS | 0 WARNINGS | i 12 NOTES
i See the limpa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.