===============================
R CMD BUILD
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* checking for file ClusterGVis/DESCRIPTION ... OK
* preparing ClusterGVis:
* 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
* looking to see if a data/datalist file should be added
* building ClusterGVis_0.99.0.tar.gz
===============================
BiocCheckGitClone('ClusterGVis')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/ClusterGVis_20250904151250/ClusterGVis
BiocVersion: 3.22
Package: ClusterGVis
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/ClusterGVis_20250904151250/ClusterGVis.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/ClusterGVis_20250904151250/ClusterGVis
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
ClusterGVis.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: Unable to read CITATION file with 'utils::readCitationFile()'
BiocCheck v1.45.18 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/3918/ClusterGVis_20250904151250/ClusterGVis.Rcheck
* using R version 4.5.1 (2025-06-13)
* 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 ClusterGVis/DESCRIPTION ... OK
* this is package ClusterGVis version 0.99.0
* 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 ClusterGVis can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [7s/7s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [7s/7s] OK
* checking loading without being on the library search path ... [7s/7s] 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 ... [26s/26s] 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 ... [5s/5s] OK
* checking data for ASCII and uncompressed saves ... WARNING
Warning: large data file saved inefficiently:
size ASCII compress
pbmc_subset.rda 3.0Mb FALSE none
* checking files in vignettes ... OK
* checking examples ... [177s/177s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
enrichCluster 147.039 2.473 149.532
getClusters 5.812 0.637 6.451
* 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: 1 WARNING
See
/home/pkgbuild/packagebuilder/workers/jobs/3918/ClusterGVis_20250904151250/ClusterGVis.Rcheck/00check.log
for details.
===============================
BiocCheck('ClusterGVis_0.99.0.tar.gz')
===============================
Installing ClusterGVis
Package installed successfully
ClusterGVis session metadata
sourceDir: /tmp/RtmpbYGsF0/file4326010581412/ClusterGVis
BiocVersion: 3.22
Package: ClusterGVis
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3918/ClusterGVis_20250904151250/ClusterGVis.BiocCheck
BiocCheckVersion: 1.45.18
sourceDir: /tmp/RtmpbYGsF0/file4326010581412/ClusterGVis
installDir: /tmp/RtmpbYGsF0/file4326032336e14
isTarBall: TRUE
platform: unix
Running BiocCheck on ClusterGVis
* 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...
* 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 (12%).
* 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:
vignette.Rmd
ERROR: Package installation calls found in vignette(s)
Found in files:
vignettes/vignette.Rmd (chunk no. 1, line 21, column 5)
vignettes/vignette.Rmd (chunk no. 1, line 22, column 14)
! WARNING: Potential package installation calls found in vignette(s)
Found in files:
vignettes/vignette.Rmd (chunk no. 1, line 21, column 5)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
vignettes/vignette.Rmd (chunk no. 3, line 105, column 56)
vignettes/vignette.Rmd (chunk no. 3, line 108, column 47)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ClusterGVis...
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
visCluster() (R/4.visCluster.R): 1425 lines
...
plot_pseudotime_heatmap2() (R/monocleHeatmap.R): 250 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/traverseTree.Rd
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
exprs.Rd
...
pseudotime.Rd
* 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; 10 lines (0%) are > 80 characters long.
First few lines:
R/monocleHeatmap.R#L241 [row ...
...
vignettes/vignette.Rmd#L104 markGenes = unique(pbmc.markers$gene)[sa ...
i NOTE: Consider multiples of 4 spaces for line indents; 1593 lines (37%) are
not.
First few lines:
R/1.getClusters.R#L39 # check datatype ...
...
vignettes/vignette.Rmd#L113 cluster.order = c(1:9)) ...
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...
! WARNING: The package already exists on CRAN. Packages submitted to
Bioconductor must be removed from CRAN before the next Bioconductor release.
* 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 v1.45.18 results
3 ERRORS | 4 WARNINGS | i 6 NOTES
i See the ClusterGVis.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.