===============================
R CMD BUILD
===============================
* checking for file wSIR/DESCRIPTION ... OK
* preparing wSIR:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package to build vignettes
* creating vignettes ... OK
* 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_0.99.2.tar.gz
===============================
BiocCheckGitClone('wSIR')
===============================
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR
BiocVersion: 3.20
Package: wSIR
PackageVersion: 0.99.2
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
src/matrixmult.o
src/RcppExports.o
src/wSIR.so
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.41.17 results
1 ERRORS | 0 WARNINGS | 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR.Rcheck
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 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 0.99.2
* 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 wSIR can be installed ... ERROR
Installation failed.
See /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR.Rcheck/00install.out for details.
* DONE
Status: 1 ERROR
See
/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR.Rcheck/00check.log
for details.
===============================
BiocCheck('wSIR_0.99.2.tar.gz')
===============================
Installing wSIR
Package installed successfully
wSIR session metadata
sourceDir: /tmp/Rtmp0D3ql2/file8e62d2d2ce2fd/wSIR
BiocVersion: 3.20
Package: wSIR
PackageVersion: 0.99.2
BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3570/wSIR_20241016170849/wSIR.BiocCheck
BiocCheckVersion: 1.41.17
sourceDir: /tmp/Rtmp0D3ql2/file8e62d2d2ce2fd/wSIR
installDir: /tmp/Rtmp0D3ql2/file8e62d3b7f6003
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...
* 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...
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 (31%).
* Checking for pinned package versions in DESCRIPTION...
* 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 wSIR...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/exploreWSIRParams.R (line 206, column 10)
* 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...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 23 lines (1%) are > 80 characters long.
First few lines:
R/calculatewSIR.R#L12 #' @param dimred String or integer scala ...
...
vignettes/wSIR_vignette.Rmd#L401 An example of a very simple application ...
i NOTE: Consider multiples of 4 spaces for line indents; 330 lines (18%) are
not.
First few lines:
R/calculatewSIR.R#L41 assay.type = " ...
...
vignettes/wSIR_vignette.Rmd#L388 optim_params ...
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 v1.41.17 results
0 ERRORS | 0 WARNINGS | 6 NOTES
i See the wSIR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.