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R CMD BUILD
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* checking for file MutSeqR/DESCRIPTION ... OK
* preparing MutSeqR:
* checking DESCRIPTION meta-information ... OK
* installing the package 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 MutSeqR_0.99.3.tar.gz
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BiocCheckGitClone('MutSeqR')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/75186e3085798c4d2b12d38325f8d6de21ccd845/MutSeqR
BiocVersion: 3.22
Package: MutSeqR
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/75186e3085798c4d2b12d38325f8d6de21ccd845/MutSeqR.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/75186e3085798c4d2b12d38325f8d6de21ccd845/MutSeqR
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 v1.45.18 results
0 ERRORS | 0 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
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* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3856/75186e3085798c4d2b12d38325f8d6de21ccd845/MutSeqR.Rcheck
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 MutSeqR/DESCRIPTION ... OK
* this is package MutSeqR version 0.99.3
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 MutSeqR 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 ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [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 ... [62s/62s] 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 ... [268s/290s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculate_mf 54.590 1.567 59.961
filter_mut 20.944 0.631 23.434
write_vcf_from_mut 20.358 0.375 21.459
plot_radar 16.194 0.398 17.380
plot_trinucleotide 15.489 0.250 16.712
plot_trinucleotide_heatmap 14.307 0.177 15.939
get_binom_ci 12.713 0.119 14.747
plot_bubbles 10.921 0.163 12.210
write_mutational_matrix 9.993 0.142 10.927
plot_lollipop 8.953 0.056 9.991
write_mutation_calling_file 8.422 0.064 13.711
import_vcf_data 7.497 0.226 9.418
import_mut_data 6.757 0.145 7.869
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [18s/18s]
[18s/18s] 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 ... [5s/4s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('MutSeqR_0.99.3.tar.gz')
===============================
Installing MutSeqR
Package installed successfully
MutSeqR session metadata
sourceDir: /tmp/RtmpA7BEPu/file38e5bb3dda75a6/MutSeqR
BiocVersion: 3.22
Package: MutSeqR
PackageVersion: 0.99.3
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/75186e3085798c4d2b12d38325f8d6de21ccd845/MutSeqR.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmpA7BEPu/file38e5bb3dda75a6/MutSeqR
installDir: /tmp/RtmpA7BEPu/file38e5bb1496b36
isTarBall: TRUE
platform: unix
Running BiocCheck on MutSeqR
* 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...
* 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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (50%).
* 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 MutSeqR...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
proast.min.R (line 262, column 24)
...
proast.min.R (line 14951, column 17)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/proast.min.R (line 81, column 13)
...
print() in R/proast.min.R (line 14931, column 9)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/proast.min.R (line 4103, column 26)
...
R/proast.min.R (line 13038, column 30)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/plot_mean_mf.r (line 132, column 10)
...
R/proast.min.R (line 14206, column 38)
! WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/proast.min.R (line 8826, 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 78
functions greater than 50 lines.
The longest 5 functions are:
f.select.m5.con() (R/proast.min.R): 1436 lines
...
f.nlminb() (R/proast.min.R): 721 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
print_ascii_art.Rd
...
signature_fitting.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 2% of man
pages use at least one of these tags.
Found in files:
signature_fitting.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; 912 lines (4%) are > 80 characters long.
First few lines:
R/bmd_proast.r#L152 #' # We will calculate the BMD for a 50% ...
...
vignettes/MutSeqR_introduction.Rmd#L1455 If an experimental variable is not
provi ...
i NOTE: Consider 4 spaces instead of tabs; 10 lines (0%) contain tabs.
First few lines:
R/model_mf.R#L109 #' 25:chr1 0:chr1 ...
...
R/spectra_comparison.R#L64 #' 50:bone_marrow 50:liver ...
i NOTE: Consider multiples of 4 spaces for line indents; 7010 lines (28%) are
not.
First few lines:
R/bmd_proast.r#L165 mf_data, ...
...
vignettes/MutSeqR_introduction.Rmd#L1223 output_format = "html_docu ...
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.
i Package is in the Support Site Watched Tags.
BiocCheck v1.45.18 results
0 ERRORS | 1 WARNINGS | i 10 NOTES
i See the MutSeqR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.