===============================
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_0.99.8.tar.gz’
===============================
BiocCheckGitClone('MutSeqR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/423538c16375c8c5928a474f835b1c97fc958095/MutSeqR
→ BiocVersion: 3.23
→ Package: MutSeqR
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/423538c16375c8c5928a474f835b1c97fc958095/MutSeqR.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/423538c16375c8c5928a474f835b1c97fc958095/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/3856/423538c16375c8c5928a474f835b1c97fc958095/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 ‘0.99.8’
* 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 ... NOTE
unable to verify current time
* 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 ... [13s/13s] 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 ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] OK
* checking whether startup messages can be suppressed ... [13s/13s] 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 ... [64s/64s] 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 ... [58s/58s] OK
* 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/5s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3856/423538c16375c8c5928a474f835b1c97fc958095/MutSeqR.Rcheck/00check.log’
for details.
===============================
BiocCheck('MutSeqR_0.99.8.tar.gz')
===============================
── Installing MutSeqR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MutSeqR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpBTools/file21d11d238dd3d2/MutSeqR
→ BiocVersion: 3.23
→ Package: MutSeqR
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/423538c16375c8c5928a474f835b1c97fc958095/MutSeqR.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/RtmpBTools/file21d11d238dd3d2/MutSeqR
→ installDir: /tmp/RtmpBTools/file21d11d6f95d893
→ 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...
* 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 15085, column 9)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/plot_mean_mf.R (line 197, column 10)
• R/proast.min.R (line 14360, column 38)
* 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
• 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; 883 lines (3%) are > 80 characters long.
First few lines:
• R/calculate_mf.R#L559 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#L62 #' 50:bone_marrow 50:liver ...
i NOTE: Consider multiples of 4 spaces for line indents; 6106 lines (24%) are
not.
First few lines:
• R/bmd_proast.R#L192 stop("Package \"withr\" needed for ...
• ...
• 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...
* 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 | ⚠ 0 WARNINGS | i 10 NOTES
i See the MutSeqR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.