===============================
R CMD BUILD
===============================
* checking for file ‘crupR/DESCRIPTION’ ... OK
* preparing ‘crupR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘crupR_0.99.4.tar.gz’
===============================
BiocCheckGitClone('crupR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR
→ BiocVersion: 3.21
→ Package: crupR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR.BiocCheck
→ BiocCheckVersion: 1.43.15
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.43.15 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/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘crupR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘crupR’ version ‘0.99.4’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 23 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* 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 ‘crupR’ can be installed ... OK
* checking installed package size ... INFO
installed size is 6.3Mb
sub-directories of 1Mb or more:
extdata 6.0Mb
* 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 ... [10s/10s] OK
* checking whether the package can be loaded with stated dependencies ... [10s/10s] OK
* checking whether the package can be unloaded cleanly ... [10s/10s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [10s/10s] OK
* checking loading without being on the library search path ... [10s/10s] 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 ... [35s/35s] 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 ... [145s/152s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
normalize 92.057 12.249 111.989
getEnhancers 10.280 1.666 11.948
getDynamics 10.140 0.272 10.415
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [69s/76s]
[70s/76s] 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 ... [4s/4s] OK
* DONE
Status: OK
===============================
BiocCheck('crupR_0.99.4.tar.gz')
===============================
── Installing crupR ────────────────────────────────────────────────────────────
✔ Package installed successfully
── crupR session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpXgKgeL/file17570d11f9f770/crupR
→ BiocVersion: 3.21
→ Package: crupR
→ PackageVersion: 0.99.4
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3413/545c02ab354f63d16645667a7d792de95aed88c2/crupR.BiocCheck
→ BiocCheckVersion: 1.43.15
→ sourceDir: /tmp/RtmpXgKgeL/file17570d11f9f770/crupR
→ installDir: /tmp/RtmpXgKgeL/file17570d7eef0327
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on crupR ──────────────────────────────────────────────────
* 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 4.4.0 to 4.5.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
GeneExpression, WholeGenome, ChipOnChip, GenePrediction, Normalization,
Clustering
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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (44%).
* 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 .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 crupR...
* Checking coding practice...
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/enhancerDynamics.R (line 86, column 14)
• ...
• R/saveFiles.R (line 51, column 14)
* 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 458, column 10)
• suppressMessages() in R/functions.R (line 592, column 9)
* 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:
• saveFiles() (R/saveFiles.R): 155 lines
• ...
• getTargets() (R/enhancerTargets.R): 62 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• saveFiles.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 12% of man
pages use at least one of these tags.
Found in files:
• saveFiles.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; 353 lines (19%) are > 80 characters long.
First few lines:
• R/enhancerDynamics.R#L4 #' The genome-wide enhancer probabilitie ...
• ...
• vignettes/crupR-vignette.Rmd#L319 Note that you could theoretically also u
...
i NOTE: Consider multiples of 4 spaces for line indents; 34 lines (2%) are not.
First few lines:
• R/functions.R#L316 2]) <= 0))), idx = idx ...
• ...
• vignettes/crupR-vignette.Rmd#L315 nearest = 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...
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 v1.43.15 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the crupR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.