===============================
R CMD BUILD
===============================
* checking for file ‘terapadog/DESCRIPTION’ ... OK
* preparing ‘terapadog’:
* 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
WARNING: directory ‘terapadog/data’ is empty
* building ‘terapadog_0.99.0.tar.gz’
===============================
BiocCheckGitClone('terapadog')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/terapadog_20241204194443/terapadog
→ BiocVersion: 3.21
→ Package: terapadog
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/terapadog_20241204194443/terapadog.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/terapadog_20241204194443/terapadog
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
• inst/.DS_Store
✖ ERROR: System files found that should not be Git tracked.
• data/.DS_Store
• terapadog.Rproj
* 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 v1.43.2 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3615/terapadog_20241204194443/terapadog.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘terapadog/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘terapadog’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
ERROR
Package suggested but not available: ‘rmakrkdown’
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/3615/terapadog_20241204194443/terapadog.Rcheck/00check.log’
for details.
===============================
BiocCheck('terapadog_0.99.0.tar.gz')
===============================
── Installing terapadog ────────────────────────────────────────────────────────
✔ Package installed successfully
── terapadog session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmprrUeL1/file3a97a232ae1b49/terapadog
→ BiocVersion: 3.21
→ Package: terapadog
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3615/terapadog_20241204194443/terapadog.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmprrUeL1/file3a97a232ae1b49/terapadog
→ installDir: /tmp/RtmprrUeL1/file3a97a275f1f077
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on terapadog ──────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (33%).
* 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 terapadog...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/preprocessing_helpers.R (line 109, column 26)
• R/terapadog.R (line 266, column 5)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• get_FCs.R (line 140, column 55)
• terapadog.R (line 184, column 53)
• terapadog.R (line 272, column 15)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/terapadog.R (line 90, column 5)
• ...
• cat() in R/terapadog.R (line 277, column 7)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/id_converter.R (line 34, column 10)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressMessages() in R/get_FCs.R (line 63, column 13)
• suppressMessages() in R/terapadog.R (line 251, column 15)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 6
functions greater than 50 lines.
The longest 5 functions are:
• terapadog() (R/terapadog.R): 281 lines
• ...
• id_converter() (R/id_converter.R): 61 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• terapadog.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; 109 lines (7%) are > 80 characters long.
First few lines:
• R/assign_Regmode.R#L5 #' regulatory mode to each gene based on ...
• ...
• vignettes/terapadog_vignette.Rmd#L497 Griss J, Viteri G, Sidiropoulos K,
Nguye ...
i NOTE: Consider multiples of 4 spaces for line indents; 374 lines (25%) are
not.
First few lines:
• R/assign_Regmode.R#L30 # Function checks padj (the padj value ...
• ...
• vignettes/terapadog_vignette.Rmd#L244 sample ...
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 v1.43.2 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 12 NOTES
i See the terapadog.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.