===============================
R CMD BUILD
===============================
* checking for file ‘CENTRE/DESCRIPTION’ ... OK
* preparing ‘CENTRE’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘CENTRE_0.99.2.tar.gz’
===============================
BiocCheckGitClone('CENTRE')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/d7aea374524128dfff1b9490e6b0bb106c9674aa/CENTRE
→ BiocVersion: 3.23
→ Package: CENTRE
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/d7aea374524128dfff1b9490e6b0bb106c9674aa/CENTRE.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/d7aea374524128dfff1b9490e6b0bb106c9674aa/CENTRE
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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...
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3927/d7aea374524128dfff1b9490e6b0bb106c9674aa/CENTRE.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘CENTRE/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CENTRE’ 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 ‘CENTRE’ 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [13s/13s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] 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 ... [38s/38s] 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 ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('CENTRE_0.99.2.tar.gz')
===============================
── Installing CENTRE ───────────────────────────────────────────────────────────
✔ Package installed successfully
── CENTRE session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpzqigVa/file15fa563738b8de/CENTRE
→ BiocVersion: 3.23
→ Package: CENTRE
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3927/d7aea374524128dfff1b9490e6b0bb106c9674aa/CENTRE.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpzqigVa/file15fa563738b8de/CENTRE
→ installDir: /tmp/RtmpzqigVa/file15fa5624afd60b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CENTRE ─────────────────────────────────────────────────
* 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 (54%).
* 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...
! WARNING: Evaluate more vignette chunks.
i 5 out of 8 code chunks = 62% unevaluated
i 0 non-exec code chunk(s) (e.g., '```r')
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CENTRE...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• functionsComputeCellType.R (line 123, column 27)
• ...
• functionsComputeCellType.R (line 194, column 27)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/centrePrediction.R (line 98, column 13)
• ...
• R/createPairs.R (line 52, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/computeCellTypeFeatures.R (line 120, column 13)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressMessages() in R/functions.R (line 199, column 5)
• suppressMessages() in R/functions.R (line 284, column 5)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 7
functions greater than 50 lines.
The longest 5 functions are:
• geneCenteredPairs() (R/functions.R): 87 lines
• ...
• centrePrediction() (R/centrePrediction.R): 65 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; 23 lines (1%) are > 80 characters long.
First few lines:
• R/functions.R#L132 # extend the enhancer region 500Kb t ...
• ...
• vignettes/CENTRE_vignette.Rmd#L252 by a `_` of the corresponding pair and t
...
i NOTE: Consider multiples of 4 spaces for line indents; 1 lines (0%) are not.
First few lines:
• vignettes/CENTRE_vignette.Rmd#L47 `computeCellTypeFeatures()` -> `centreC ...
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 v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 9 NOTES
i See the CENTRE.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.