===============================
R CMD BUILD
===============================
* checking for file MutSeqR/DESCRIPTION ... OK
* preparing MutSeqR:
* 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 MutSeqR_0.99.5.tar.gz
===============================
BiocCheckGitClone('MutSeqR')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/afcde7461cb92de63adf5190826f58f51710a673/MutSeqR
BiocVersion: 3.23
Package: MutSeqR
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/afcde7461cb92de63adf5190826f58f51710a673/MutSeqR.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/afcde7461cb92de63adf5190826f58f51710a673/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...
* Checking that provided CITATION file is correctly formatted...
BiocCheck v1.47.7 results
0 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/3856/afcde7461cb92de63adf5190826f58f51710a673/MutSeqR.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 MutSeqR/DESCRIPTION ... OK
* this is package MutSeqR version 0.99.5
* 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 ... WARNING
Invalid citation information in inst/CITATION:
Warning message:
In utils::packageDescription(basename(dir), dirname(dir)) :
DESCRIPTION file of package 'MutSeqR' is missing or broken
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] ERROR
Loading this package had a fatal error status code 1
Loading log:
Error in library(MutSeqR) : there is no package called MutSeqR
Execution halted
* DONE
Status: 1 ERROR, 1 WARNING
See
/home/pkgbuild/packagebuilder/workers/jobs/3856/afcde7461cb92de63adf5190826f58f51710a673/MutSeqR.Rcheck/00check.log
for details.
===============================
BiocCheck('MutSeqR_0.99.5.tar.gz')
===============================
Installing MutSeqR
Package installed successfully
MutSeqR session metadata
sourceDir: /tmp/RtmpU90DD1/file1af1a879398c91/MutSeqR
BiocVersion: 3.23
Package: MutSeqR
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/afcde7461cb92de63adf5190826f58f51710a673/MutSeqR.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/RtmpU90DD1/file1af1a879398c91/MutSeqR
installDir: /tmp/RtmpU90DD1/file1af1a8233c726e
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...
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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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)
...
write_nice_excel.R (line 128, column 16)
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 188, 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 81
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.
render_report.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; 870 lines (3%) are > 80 characters long.
First few lines:
R/calculate_mf.R#L565 if (subtype_resolution %in% c("b ...
...
vignettes/MutSeqR_introduction.Rmd#L1449 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#L107 #' 25:chr1 0:chr1 ...
...
R/spectra_comparison.R#L64 #' 50:bone_marrow 50:liver ...
i NOTE: Consider multiples of 4 spaces for line indents; 6145 lines (24%) are
not.
First few lines:
R/bmd_proast.R#L203 bmr_sd <- as.numeric(adjust_bmr_to_gro ...
...
vignettes/MutSeqR_introduction.Rmd#L1443 Also includes recurrent mutations
wit ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/experiment
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/workflows
* 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 v1.47.7 results
0 ERRORS | 1 WARNINGS | i 10 NOTES
i See the MutSeqR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.