===============================
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_0.99.2.tar.gz
===============================
BiocCheckGitClone('mesa')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/mesa
BiocVersion: 3.23
Package: mesa
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/mesa.BiocCheck
BiocCheckVersion: 1.49.6
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/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/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/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 v1.49.6 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/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/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: 2026-05-19 09:45:54 UTC
* using option --no-vignettes
* checking for file mesa/DESCRIPTION ... OK
* this is package mesa version 0.99.2
* 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 ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking whether startup messages can be suppressed ... [11s/11s] 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 ... [42s/42s] 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 ... [14s/14s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [147s/147s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculateCGEnrichment 5.084 0.939 6.031
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('mesa_0.99.2.tar.gz')
===============================
Installing mesa
Package installed successfully
mesa session metadata
sourceDir: /tmp/RtmpV9fwRM/file3086ea3659187e/mesa
BiocVersion: 3.23
Package: mesa
PackageVersion: 0.99.2
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/ec003e99afbe1f85c5aa644a2ac6d43e4513e067/mesa.BiocCheck
BiocCheckVersion: 1.49.6
sourceDir: /tmp/RtmpV9fwRM/file3086ea3659187e/mesa
installDir: /tmp/RtmpV9fwRM/file3086ea6d7bdf21
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...
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
addBamCoveragePairedAndUnpaired.Rd
...
writeDMRsToExcel.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
Found in files:
addHMMcopyCNV.Rd
...
writeDMRsToExcel.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; 1134 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...
i Maintainer is registered at support site.
ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
BiocCheck v1.49.6 results
2 ERRORS | 0 WARNINGS | i 7 NOTES
i See the mesa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.