===============================
R CMD BUILD
===============================
* checking for file ‘carnation/DESCRIPTION’ ... OK
* preparing ‘carnation’:
* 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 ‘carnation_0.99.1.tar.gz’
===============================
BiocCheckGitClone('carnation')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3973/carnation_20251202174728/carnation
→ BiocVersion: 3.23
→ Package: carnation
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3973/carnation_20251202174728/carnation.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3973/carnation_20251202174728/carnation
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.47.1 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/3973/carnation_20251202174728/carnation.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘carnation/DESCRIPTION’ ... OK
* this is package ‘carnation’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 31 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 ‘carnation’ 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [16s/16s] OK
* checking whether startup messages can be suppressed ... [16s/16s] 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 ... [63s/63s] 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 ... NONE
* 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('carnation_0.99.1.tar.gz')
===============================
── Installing carnation ────────────────────────────────────────────────────────
✔ Package installed successfully
── carnation session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpP0QQBd/file846076e087958/carnation
→ BiocVersion: 3.23
→ Package: carnation
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3973/carnation_20251202174728/carnation.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpP0QQBd/file846076e087958/carnation
→ installDir: /tmp/RtmpP0QQBd/file84607cea7ea0
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on carnation ──────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.3.0 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 that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
i NOTE: No 'fnd' role found in Authors@R. If the work is supported by a grant,
consider adding the 'fnd' role to the list of authors.
* 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:
• carnation.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of carnation...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/app.R (line 1496, column 20)
• ...
• R/functions.R (line 841, column 25)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• enrich-plots.R (line 232, column 55)
• ...
• upset-plot.R (line 643, column 32)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/buttons.R (line 166, column 13)
• ...
• cat() in R/functions.R (line 631, column 13)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/functions.R (line 1289, column 13)
• ...
• R/functions.R (line 1297, column 27)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/access-functions.R (line 15, column 9)
• ...
• R/scatter-plot.R (line 398, column 21)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/settings.R (line 195, column 16)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 4 times:
• T in R/functions.R (line 1824, column 38)
• ...
• T in R/ma-plot.R (line 192, column 54)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
• suppressMessages() in R/functions.R (line 670, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 74
functions greater than 50 lines.
The longest 5 functions are:
• run_carnation() (R/app.R): 1690 lines
• ...
• loadDataServer() (R/load-new-data.R): 1004 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/add_metadata.Rd
• ...
• man/upsetPlotUI.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• add_metadata.Rd
• ...
• upsetPlotUI.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 593 lines (4%) are > 80 characters long.
First few lines:
• R/access-functions.R#L37 #' @param al list with access settings; ...
• ...
• vignettes/carnation.Rmd#L588 - You can also quickly add genes to the ...
i NOTE: Consider multiples of 4 spaces for line indents; 6782 lines (40%) are
not.
First few lines:
• R/access-functions.R#L11 if(Sys.getenv('CARNATION_ACCESS_YAML') ...
• ...
• vignettes/carnation.Rmd#L620 passphrase = 'admin_passphrase' ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | i 16 NOTES
i See the carnation.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.