===============================
R CMD BUILD
===============================
* checking for file ‘wSIR/DESCRIPTION’ ... OK
* preparing ‘wSIR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
Warning: ‘inst/doc’ files
‘wSIR_vignette.Rmd’, ‘wSIR_vignette.html’, ‘wSIR_vignette.R’
ignored as vignettes have been rebuilt.
Run R CMD build with --no-build-vignettes to prevent rebuilding.
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* looking to see if a ‘data/datalist’ file should be added
* building ‘wSIR_0.99.4.tar.gz’
===============================
BiocCheckGitClone('wSIR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR
→ BiocVersion: 3.23
→ Package: wSIR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
✖ ERROR: System files found that should not be Git tracked.
• tests/.DS_Store
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
✖ ERROR: Remove 'inst/doc' folder from the package source
* Checking if DESCRIPTION is well formatted...
* Checking NAMESPACE...
* Checking for valid maintainer...
✖ ERROR: Use Authors@R field not Author/Maintainer fields. Do not use both.
* 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 v1.47.18 results ──────────────────────────────────────────────────
✖ 3 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/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR.Rcheck’
* using R Under development (unstable) (2026-01-15 r89304)
* 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 ‘wSIR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘wSIR’ version ‘0.99.4’
* 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 ‘wSIR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04) 13.3.0’
* checking installed package size ... INFO
installed size is 5.2Mb
sub-directories of 1Mb or more:
data 2.2Mb
doc 1.8Mb
libs 1.0Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [9s/9s] OK
* checking whether the package can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [9s/9s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [29s/29s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [2s/2s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... OK
* checking compiled code ... NOTE
Note: information on .o files is not available
File ‘/home/pkgbuild/packagebuilder/workers/jobs/3570/R-libs/wSIR/libs/wSIR.so’:
Found ‘abort’, possibly from ‘abort’ (C)
Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs nor [v]sprintf. The detected symbols are linked into
the code but might come from libraries and not actually be called.
See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [233s/233s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
exploreWSIRParams 124.511 1.130 125.698
plotUmapFromWSIR 29.645 0.170 29.817
generateUmapFromWSIR 26.728 0.342 27.073
wSIR 19.750 0.143 19.895
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [11s/11s]
[11s/11s] 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 ... [3s/3s] OK
* DONE
Status: 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR.Rcheck/00check.log’
for details.
===============================
BiocCheck('wSIR_0.99.4.tar.gz')
===============================
── Installing wSIR ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── wSIR session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpPYG3wT/file13ec2f11f9feb/wSIR
→ BiocVersion: 3.23
→ Package: wSIR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3570/3e83dcd1880d8a0a2d3ee70867a30bc41b5663be/wSIR.BiocCheck
→ BiocCheckVersion: 1.47.18
→ sourceDir: /tmp/RtmpPYG3wT/file13ec2f11f9feb/wSIR
→ installDir: /tmp/RtmpPYG3wT/file13ec2f557f8c3e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on wSIR ───────────────────────────────────────────────────
* 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 4.4.0 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...
! WARNING: Invalid BiocViews term(s):
• 'CellBasedArrays': Did you mean 'CellBasedAssays'?
* Checking for recommended biocViews...
i NOTE: Consider adding these automatically suggested biocViews:
CellBasedAssays
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 (33%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• wSIR_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of wSIR...
* Checking coding practice...
* 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 2
functions greater than 50 lines.
The longest 5 functions are:
• exploreWSIRParams() (R/exploreWSIRParams.R): 120 lines
• calculatewSIR() (R/calculatewSIR.R): 60 lines
* Checking man page documentation...
* 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; 34 lines (2%) are > 80 characters long.
First few lines:
• R/calculatewSIR.R#L12 #' @param dimred String or integer scala ...
• ...
• vignettes/wSIR_vignette.Rmd#L400 An example of a very simple application ...
i NOTE: Consider multiples of 4 spaces for line indents; 111 lines (6%) are
not.
First few lines:
• R/calculatewSIR.R#L41 assay.type = " ...
• ...
• vignettes/wSIR_vignette.Rmd#L408 k = 10) ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 504 Gateway
Timeout.
── BiocCheck v1.47.18 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 7 NOTES
i See the wSIR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.