===============================
R CMD BUILD
===============================
* checking for file ClonalSim/DESCRIPTION ... OK
* preparing ClonalSim:
* 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
WARNING: directory ClonalSim/inst/scripts is empty
* building ClonalSim_0.99.0.tar.gz
===============================
BiocCheckGitClone('ClonalSim')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim
BiocVersion: 3.23
Package: ClonalSim
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
ClonalSim.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...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
BiocCheck v1.47.7 results
1 ERRORS | 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim.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 ClonalSim/DESCRIPTION ... OK
* checking extension type ... Package
* this is package ClonalSim version 0.99.0
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Package suggested but not available: fishplot
The suggested packages are required for a complete check.
Checking can be attempted without them by setting the environment
variable _R_CHECK_FORCE_SUGGESTS_ to a false value.
See section The DESCRIPTION file in the Writing R Extensions
manual.
* DONE
Status: 1 ERROR
See
/home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim.Rcheck/00check.log
for details.
===============================
BiocCheck('ClonalSim_0.99.0.tar.gz')
===============================
Installing ClonalSim
Package installed successfully
ClonalSim session metadata
sourceDir: /tmp/Rtmpld6Hip/file1f92686279111f/ClonalSim
BiocVersion: 3.23
Package: ClonalSim
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4030/ClonalSim_20251211142439/ClonalSim.BiocCheck
BiocCheckVersion: 1.47.7
sourceDir: /tmp/Rtmpld6Hip/file1f92686279111f/ClonalSim
installDir: /tmp/Rtmpld6Hip/file1f926843f5ad23
isTarBall: TRUE
platform: unix
Running BiocCheck on ClonalSim
* 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 (40%).
* 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...
* Checking for library/require of ClonalSim...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
simulateTumor.R (line 242, column 52)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/noise_model.R (line 187, column 10)
! WARNING: Remove set.seed usage (found 1 times)
set.seed() in R/simulateTumor.R (line 118, 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 3
functions greater than 50 lines.
The longest 5 functions are:
simulateTumor() (R/simulateTumor.R): 209 lines
_anonymous_.141() (R/methods.R): 140 lines
.generate_mutations() (R/simulateTumor.R): 64 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/accessors.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 22% of man
pages use at least one of these tags.
Found in files:
plot-ClonalSimData-missing-method.Rd
...
toVCF.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
plot-ClonalSimData-missing-method.Rd
...
toVCF.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; 31 lines (2%) are > 80 characters long.
First few lines:
R/AllClasses.R#L106 if (any(object@mutations$VAF < 0 | o ...
...
vignettes/Introduction_to_ClonalSim.Rmd#L330 This creates a characteristic
peak at VA ...
i NOTE: Consider multiples of 4 spaces for line indents; 483 lines (25%) are
not.
First few lines:
R/accessors.R#L19 stopifnot(inherits(object, "ClonalSimD ...
...
vignettes/Introduction_to_ClonalSim.Rmd#L453 spatial and temporal patterns of
tumo ...
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...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
BiocCheck v1.47.7 results
1 ERRORS | 2 WARNINGS | i 9 NOTES
i See the ClonalSim.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.