===============================
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_0.99.3.tar.gz’
===============================
BiocCheckGitClone('mesa')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/a1e3686a6af412f4c28773d63cf2285b3d299827/mesa
→ BiocVersion: 3.23
→ Package: mesa
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/a1e3686a6af412f4c28773d63cf2285b3d299827/mesa.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/a1e3686a6af412f4c28773d63cf2285b3d299827/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/a1e3686a6af412f4c28773d63cf2285b3d299827/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 v1.49.12 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/a1e3686a6af412f4c28773d63cf2285b3d299827/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: 2026-06-11 15:45:41 UTC
* using option ‘--no-vignettes’
* checking for file ‘mesa/DESCRIPTION’ ... OK
* this is package ‘mesa’ version ‘0.99.3’
* 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 ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [10s/10s] OK
* checking whether startup messages can be suppressed ... [11s/11s] 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 ... [38s/38s] 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 ... [243s/243s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
summariseDMRsByGene 52.150 1.544 53.700
getDimRed 21.701 0.194 21.893
plotUMAP 12.136 0.553 12.688
writeDMRsToBed 8.756 0.143 8.902
writeDMRsToExcel 8.525 0.188 8.715
calculateCGEnrichmentGRanges 7.465 0.514 7.980
plotDimRed 7.046 0.641 7.687
calculateCGEnrichment 4.129 0.906 5.036
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('mesa_0.99.3.tar.gz')
===============================
── Installing mesa ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── mesa session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpN6KURc/file3f454a5c4991ba/mesa
→ BiocVersion: 3.23
→ Package: mesa
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4211/a1e3686a6af412f4c28773d63cf2285b3d299827/mesa.BiocCheck
→ BiocCheckVersion: 1.49.12
→ sourceDir: /tmp/RtmpN6KURc/file3f454a5c4991ba/mesa
→ installDir: /tmp/RtmpN6KURc/file3f454a33a432cb
→ 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...
* 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 43
functions greater than 50 lines.
The longest 5 functions are:
• getDimRed() (R/PCA.R): 624 lines
• ...
• plotDimRed() (R/PCA.R): 286 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. 11% 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...
* 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...
! WARNING: Unable to retrieve email info from the Support Site: Failed to
perform HTTP request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout
was reached [support.bioconductor.org]: Operation timed out after 15002
milliseconds with 0 bytes received
── BiocCheck v1.49.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 6 NOTES
i See the mesa.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.