===============================
R CMD BUILD
===============================
* checking for file damidBind/DESCRIPTION ... OK
* preparing damidBind:
* 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
* building damidBind_0.99.4.tar.gz
===============================
BiocCheckGitClone('damidBind')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20251112074202/damidBind
BiocVersion: 3.22
Package: damidBind
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20251112074202/damidBind.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20251112074202/damidBind
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...
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 v1.47.1 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/3893/damidBind_20251112074202/damidBind.Rcheck
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 damidBind/DESCRIPTION ... OK
* checking extension type ... Package
* this is package damidBind version 0.99.4
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 damidBind can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... [15s/15s] OK
* checking whether the package can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [46s/46s] 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 ... [116s/85s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
analyse_go_enrichment 16.245 1.141 11.663
plot_volcano 15.536 1.465 10.612
plot_venn 13.461 1.535 8.659
differential_binding 12.957 1.474 8.507
load_data_peaks 12.990 1.353 8.406
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [54s/54s]
[54s/54s] 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/3s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20251112074202/damidBind.Rcheck/00check.log
for details.
===============================
BiocCheck('damidBind_0.99.4.tar.gz')
===============================
Installing damidBind
Package installed successfully
damidBind session metadata
sourceDir: /tmp/RtmpdspV1K/file355818284a1a4a/damidBind
BiocVersion: 3.22
Package: damidBind
PackageVersion: 0.99.4
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20251112074202/damidBind.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpdspV1K/file355818284a1a4a/damidBind
installDir: /tmp/RtmpdspV1K/file3558181c2646e0
isTarBall: TRUE
platform: unix
Running BiocCheck on damidBind
* 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...
Warning in readLines(con) :
URL 'https://bioconductor.org/js/versions.js': status was 'SSL connect error'
* 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...
Warning: unable to access index for repository https://bioconductor.org/packages/3.22/bioc/src/contrib:
cannot open URL 'https://bioconductor.org/packages/3.22/bioc/src/contrib/PACKAGES'
! WARNING: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* 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 damidBind...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
print() in R/analyse_go_terms.R (line 387, column 9)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1 times)
suppressWarnings() in R/granges_functions.R (line 65, column 20)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 21
functions greater than 50 lines.
The longest 5 functions are:
differential_binding() (R/limma_functions.R): 121 lines
...
plot_venn() (R/plot_venn.R): 102 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
browse_igv_regions.Rd
get_ensdb_genes.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 9% of man
pages use at least one of these tags.
Found in files:
browse_igv_regions.Rd
get_ensdb_genes.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; 542 lines (12%) are > 80 characters long.
First few lines:
R/AllClasses.R#L5 #' by \code{\link{differential_binding}} ...
...
vignettes/damidBind_vignette.Rmd#L407 * `expressed(object, condition, fdr =
0. ...
i NOTE: Consider multiples of 4 spaces for line indents; 37 lines (1%) are not.
First few lines:
R/AllClasses.R#L77 slots = c( ...
...
damidBind/NAMESPACE#L40 icon, HTML, tags, numericInpu ...
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 damidBind.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.