===============================
R CMD BUILD
===============================
* checking for file sigvar/DESCRIPTION ... OK
* preparing sigvar:
* 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 sigvar_0.99.0.tar.gz
===============================
BiocCheckGitClone('sigvar')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4171/sigvar_20260323171401/sigvar
BiocVersion: 3.23
Package: sigvar
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4171/sigvar_20260323171401/sigvar.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4171/sigvar_20260323171401/sigvar
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
sigvar.Rproj
* 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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.20 results
1 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/4171/sigvar_20260323171401/sigvar.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-23 17:19:23 UTC
* using option --no-vignettes
* checking for file sigvar/DESCRIPTION ... OK
* this is package sigvar version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 sigvar 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 ... [12s/12s] 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 ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [35s/35s] 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 contents of data directory ... OK
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking R/sysdata.rda ... OK
* checking files in vignettes ... OK
* checking examples ... [32s/32s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [25s/25s]
[25s/25s] 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 ... [6s/6s] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Something's wrong--perhaps a missing \item.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
! LaTeX Error: Something's wrong--perhaps a missing \item.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
...
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING
See
/home/pkgbuild/packagebuilder/workers/jobs/4171/sigvar_20260323171401/sigvar.Rcheck/00check.log
for details.
===============================
BiocCheck('sigvar_0.99.0.tar.gz')
===============================
Installing sigvar
Package installed successfully
sigvar session metadata
sourceDir: /tmp/Rtmpm7xpSl/file16dd0f68d0a6e7/sigvar
BiocVersion: 3.23
Package: sigvar
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4171/sigvar_20260323171401/sigvar.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/Rtmpm7xpSl/file16dd0f68d0a6e7/sigvar
installDir: /tmp/Rtmpm7xpSl/file16dd0f775ed8b
isTarBall: TRUE
platform: unix
Running BiocCheck on sigvar
* 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 3.5 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...
i NOTE: Consider adding these automatically suggested biocViews: DataImport
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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (23%).
* 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:
carcinogen_figure.Rmd
...
tutorial.Rmd
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
vignettes/carcinogen_figure.Rmd
...
vignettes/tutorial.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of sigvar...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/data_vis_functions.R (line 30, column 15)
...
R/process_relab_matrices.R (line 33, column 15)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
bootstrap.R (line 177, column 18)
...
process_relab_matrices.R (line 155, column 54)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/bootstrap.R (line 100, column 10)
...
R/process_relab_matrices.R (line 165, column 15)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/process_relab_matrices.R (line 154, column 15)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 17 times:
T in R/fava_functions.R (line 521, column 5)
...
T in R/stats_functions.R (line 80, column 36)
! WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/bootstrap.R (line 67, column 5)
* 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 14
functions greater than 50 lines.
The longest 5 functions are:
pairwise_comparison() (R/bootstrap.R): 389 lines
...
plot_SBS_spectrum() (R/data_vis_functions.R): 92 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/time_weights.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; 599 lines (12%) are > 80 characters long.
First few lines:
R/bootstrap.R#L2 #' Statistically compare the within-samp ...
...
vignettes/tutorial.Rmd#L334 This concludes the tutorial on the *sigv ...
i NOTE: Consider multiples of 4 spaces for line indents; 1386 lines (28%) are
not.
First few lines:
R/bootstrap.R#L58 # To appease R cmd check ...
...
vignettes/tutorial.Rmd#L320 seed = 1) ...
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 v1.47.20 results
2 ERRORS | 3 WARNINGS | i 13 NOTES
i See the sigvar.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.