===============================
R CMD BUILD
===============================
* checking for file CONCERTDR/DESCRIPTION ... OK
* preparing CONCERTDR:
* 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
* building CONCERTDR_0.99.0.tar.gz
===============================
BiocCheckGitClone('CONCERTDR')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4205/CONCERTDR_20260330160624/CONCERTDR
BiocVersion: 3.23
Package: CONCERTDR
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4205/CONCERTDR_20260330160624/CONCERTDR.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4205/CONCERTDR_20260330160624/CONCERTDR
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/4205/CONCERTDR_20260330160624/CONCERTDR/.gitignore'
* 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 v1.47.20 results
0 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/4205/CONCERTDR_20260330160624/CONCERTDR.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-30 16:07:42 UTC
* using option --no-vignettes
* checking for file CONCERTDR/DESCRIPTION ... OK
* checking extension type ... Package
* this is package CONCERTDR 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 CONCERTDR 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 ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking whether startup messages can be suppressed ... [0s/0s] 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 ... [5s/5s] 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 ... [6s/6s] OK
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [90s/90s]
[90s/90s] 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 ... [5s/5s] OK
* DONE
Status: OK
===============================
BiocCheck('CONCERTDR_0.99.0.tar.gz')
===============================
Installing CONCERTDR
Package installed successfully
CONCERTDR session metadata
sourceDir: /tmp/Rtmp45Tpfr/file1a7f583c9e5a84/CONCERTDR
BiocVersion: 3.23
Package: CONCERTDR
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4205/CONCERTDR_20260330160624/CONCERTDR.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/Rtmp45Tpfr/file1a7f583c9e5a84/CONCERTDR
installDir: /tmp/Rtmp45Tpfr/file1a7f58594d17a4
isTarBall: TRUE
platform: unix
Running BiocCheck on CONCERTDR
* 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 (25%).
* 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 CONCERTDR...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/cmap_subset.R (line 196, column 10)
...
R/signature_matching.R (line 630, column 54)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 12 times)
suppressWarnings() in R/cmap_visualization.R (line 232, column 24)
...
suppressWarnings() in R/signature_matching.R (line 192, column 19)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 12
functions greater than 50 lines.
The longest 5 functions are:
annotate_drug_results() (R/result_summary.R): 410 lines
...
extract_cmap_data_from_siginfo() (R/cmap_subset.R): 188 lines
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 21% of man
pages use at least one of these tags.
Found in files:
annotate_drug_results.Rd
...
subset_siginfo_beta.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
extract_cmap_data_from_siginfo.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; 231 lines (6%) are > 80 characters long.
First few lines:
R/cmap_extract.R#L3 #' @description Functions to extract exp ...
...
vignettes/CONCERT_DR.Rmd#L377 CONCERTDR.gctx_file = file.pat ...
i NOTE: Consider multiples of 4 spaces for line indents; 1500 lines (39%) are
not.
First few lines:
R/cmap_extract.R#L17 for (p in paths) { ...
...
vignettes/CONCERT_DR.Rmd#L400 landmark = TRUE ...
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 v1.47.20 results
1 ERRORS | 0 WARNINGS | i 9 NOTES
i See the CONCERTDR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.