===============================
R CMD BUILD
===============================
* checking for file ‘mesa/DESCRIPTION’ ... OK
* preparing ‘mesa’:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘mesa_0.99.1.tar.gz’
===============================
BiocCheckGitClone('mesa')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa
→ BiocVersion: 3.23
→ Package: mesa
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* Checking NAMESPACE...
* Checking for valid maintainer...
* Checking CITATION...
i NOTE: (Optional) CITATION file not found. Only include a CITATION file if
there is a preprint or publication for this Bioconductor package. Note that
Bioconductor packages are not required to have a CITATION file but it is useful
both for users and for tracking Bioconductor project-wide metrics. When
including a CITATION file, add the publication using the 'doi' argument of
'bibentry()'.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-04 17:26:04 UTC
* using option ‘--no-vignettes’
* checking for file ‘mesa/DESCRIPTION’ ... OK
* this is package ‘mesa’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 36 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 whether package ‘mesa’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.6Mb
sub-directories of 1Mb or more:
R 1.0Mb
data 4.0Mb
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [9s/9s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking whether startup messages can be suppressed ... [10s/10s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: ‘qsea’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
Unexported objects imported by ':::' calls:
‘janitor:::remove_message’ ‘qsea:::addParameters’
‘qsea:::checkSamples’ ‘qsea:::getGenome’ ‘qsea:::makeGenomeWindows’
‘qsea:::setCNV’ ‘qsea:::setCounts’ ‘qsea:::setLibrary’
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [37s/37s] OK
* checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [13s/13s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('mesa_0.99.1.tar.gz')
===============================
── Installing mesa ─────────────────────────────────────────────────────────────
[9m/12m] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
makeQset 81.853 12.549 94.414
annotateWindows 82.532 1.738 84.277
plotGenomicFeatureDistribution 71.688 2.933 74.624
getGenomicFeatureDistribution 57.936 0.664 58.608
getDimRed 28.615 0.119 28.730
plotUMAP 14.358 0.211 14.569
summariseDMRsByGene 11.180 0.364 11.544
plotGeneHeatmap 9.429 0.770 144.708
writeDMRsToBed 8.651 0.092 8.744
writeDMRsToExcel 8.627 0.062 8.690
plotDimRed 8.041 0.047 8.088
calculateCGEnrichmentGRanges 6.280 0.370 6.651
plotRegionsHeatmap 5.099 0.033 5.132
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’✔ Package installed successfully
── mesa session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpG6HUFZ/file2551df6f48bb6b/mesa
→ BiocVersion: 3.23
→ Package: mesa
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/mesa_20260504171600/mesa.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpG6HUFZ/file2551df6f48bb6b/mesa
→ installDir: /tmp/RtmpG6HUFZ/file2551df884b8a8
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on mesa ───────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* Checking version number...
* Checking for version number mismatch...
* Checking new package version number...
* Checking R version dependency...
i NOTE: Update R version dependency from 4.5.0 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...
* 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 (37%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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:
• data-and-qc.Rmd
• ...
• pca.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of mesa...
* 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 36
functions greater than 50 lines.
The longest 5 functions are:
• getDimRed() (R/PCA.R): 468 lines
• ...
• plotDimRed() (R/PCA.R): 207 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• addBamCoveragePairedAndUnpaired.Rd
• ...
• runHMMCopy.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 5% of man
pages use at least one of these tags.
Found in files:
• addHMMcopyCNV.Rd
• ...
• setMesaParallel.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• addHMMcopyCNV.Rd
• ...
• setMesaParallel.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; 1137 lines (9%) are > 80 characters long.
First few lines:
• R/alterQset.R#L54 if(length(intersect(colnames(regions ...
• ...
• vignettes/pca.Rmd#L402 As a final note, we state that UMAPs sho ...
i NOTE: Consider multiples of 4 spaces for line indents; 2938 lines (22%) are
not.
First few lines:
• R/alterQset.R#L53 if(is.data.frame(regionsToOverlap)) { ...
• ...
• vignettes/pca.Rmd#L399 plotUMAP(colour = "group") ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the mesa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.