===============================
R CMD BUILD
===============================
* 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_0.99.2.tar.gz’
===============================
BiocCheckGitClone('MutSeqR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/MutSeqR_20250922171543/MutSeqR
→ BiocVersion: 3.22
→ Package: MutSeqR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/MutSeqR_20250922171543/MutSeqR.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/MutSeqR_20250922171543/MutSeqR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• MutSeqR.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...
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 ──────────────────────────────────────────────────
✖ 1 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/3856/MutSeqR_20250922171543/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 ‘0.99.2’
* 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 ... [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 ... [11s/11s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking whether startup messages can be suppressed ... [11s/11s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘GenomeInfoDb’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [60s/60s] 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 ... [469s/481s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
calculate_mf 129.505 1.755 134.300
model_mf 83.356 0.715 84.538
bmd_proast 27.912 1.461 30.482
filter_mut 27.392 0.901 28.855
plot_trinucleotide_heatmap 14.973 0.247 15.721
plot_mean_mf 14.468 0.390 15.415
plot_radar 13.975 0.112 14.566
spectra_comparison 13.783 0.101 14.544
plot_spectra 13.193 0.582 14.288
plot_trinucleotide 13.275 0.333 14.076
get_binom_ci 11.370 0.271 12.201
plot_mf 11.454 0.080 12.012
plot_bubbles 9.594 0.116 10.258
plot_lollipop 8.736 0.032 9.287
write_mutational_matrix 8.709 0.046 9.279
write_mutation_calling_file 8.238 0.034 8.963
import_vcf_data 7.615 0.129 8.270
import_mut_data 6.739 0.127 7.427
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/17s]
[17s/17s] 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 ... [4s/4s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3856/MutSeqR_20250922171543/MutSeqR.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('MutSeqR_0.99.2.tar.gz')
===============================
── Installing MutSeqR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── MutSeqR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp5QjSTH/file20f2bb43a2a5cc/MutSeqR
→ BiocVersion: 3.22
→ Package: MutSeqR
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3856/MutSeqR_20250922171543/MutSeqR.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmp5QjSTH/file20f2bb43a2a5cc/MutSeqR
→ installDir: /tmp/Rtmp5QjSTH/file20f2bb7ae2ae0a
→ 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 3.5.0 to 4.5.0
* 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...
✖ ERROR: Add biocViews other than Software
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 (48%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
✖ ERROR: Avoid using install, biocLite, install.packages, or update.packages
Found in files:
• install() in R/install_ref_genome.R (line 87, column 18)
• install.packages() in R/render_report.R (line 24, column 5)
• install.packages() in R/render_report.R (line 29, column 5)
* Checking for library/require of MutSeqR...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/filter_mut.r (line 307, column 53)
• ...
• R/reverse_complement.R (line 23, column 3)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• model_mf.R (line 412, column 13)
• ...
• write_nice_excel.R (line 140, column 53)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/model_mf.R (line 356, column 3)
• ...
• cat() in R/signature_fitting.R (line 116, column 7)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/proast.min.R (line 3906, column 34)
• ...
• R/sidak.R (line 23, column 25)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/calculate_mf.R (line 352, column 10)
• ...
• R/signature_fitting.R (line 193, column 11)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/calculate_mf.R (line 353, column 7)
• ...
• R/proast.min.R (line 13396, column 38)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 305 times:
• T in R/proast.min.R (line 85, column 49)
• ...
• F in R/spectra_comparison.R (line 190, column 81)
! WARNING: Remove set.seed usage (found 2 times)
• set.seed() in R/proast.min.R (line 8463, column 5)
• set.seed() in R/spectra_comparison.R (line 159, column 7)
! WARNING: .Deprecated / .Defunct usage (found 1 times)
• .Deprecated() in R/bmd_proast.r (line 366, column 3)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 5 times)
• suppressWarnings() in R/import_vcf_data.R (line 218, column 19)
• ...
• suppressWarnings() in R/write_sigprofiler_input.R (line 175, column 17)
* 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.quick.con() (R/proast.min.R): 576 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/bmd_toxicr.Rd
• ...
• man/setup_mutseqr_python.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• annotate_cpg_sites.Rd
• ...
• subtype_list.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 8% of man
pages use at least one of these tags.
Found in files:
• signature_fitting.Rd
• ...
• write_vcf_from_mut.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• signature_fitting.Rd
• ...
• write_vcf_from_mut.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; 1005 lines (4%) are > 80 characters long.
First few lines:
• R/calculate_mf.R#L361 ". Variation_types outside of this ...
• ...
• vignettes/MutSeqR_introduction.Rmd#L2891 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#L62 #' 50:bone_marrow 50:liver ...
i NOTE: Consider multiples of 4 spaces for line indents; 6704 lines (27%) are
not.
First few lines:
• R/bmd_proast.r#L169 mf_data, ...
• ...
• vignettes/MutSeqR_introduction.Rmd#L2697 the scientific name. Ex. "Mouse" or
"Mu ...
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 ──────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 4 WARNINGS | i 15 NOTES
i See the MutSeqR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.