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R CMD BUILD
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* 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_0.99.0.tar.gz’
===============================
BiocCheckGitClone('damidBind')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20250819184745/damidBind
→ BiocVersion: 3.22
→ Package: damidBind
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20250819184745/damidBind.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20250819184745/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 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 v1.45.12 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_20250819184745/damidBind.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 24 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 ... 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 ... [13s/13s] OK
* checking whether the package can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the package can be unloaded cleanly ... [12s/12s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [13s/13s] OK
* checking loading without being on the library search path ... [13s/13s] 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 ... [42s/42s] 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 ... [70s/60s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_volcano 11.450 1.102 10.560
analyse_go_enrichment 8.587 0.952 7.584
differential_binding 5.322 0.944 4.215
plot_venn 5.339 0.873 4.216
load_data_peaks 5.249 0.924 4.163
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [33s/33s]
[33s/33s] 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 ... [3s/3s] OK
* DONE
Status: OK
===============================
BiocCheck('damidBind_0.99.0.tar.gz')
===============================
── Installing damidBind ────────────────────────────────────────────────────────
✔ Package installed successfully
── damidBind session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpL4Tfeq/file1db6c76f3d6a9e/damidBind
→ BiocVersion: 3.22
→ Package: damidBind
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3893/damidBind_20250819184745/damidBind.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/RtmpL4Tfeq/file1db6c76f3d6a9e/damidBind
→ installDir: /tmp/RtmpL4Tfeq/file1db6c716e490a4
→ 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...
* 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 (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 damidBind...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• granges_functions.R (line 132, column 23)
• load_data.R (line 54, column 47)
• load_data.R (line 55, column 59)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/analyse_go_terms.R (line 355, column 9)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
• suppressWarnings() in R/granges_functions.R (line 66, column 16)
• suppressWarnings() in R/granges_functions.R (line 200, column 20)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 13
functions greater than 50 lines.
The longest 5 functions are:
• plot_volcano() (R/plot_volcano.R): 333 lines
• ...
• prep_data_for_differential_analysis()
(R/prep_data_for_differential_analysis.R): 103 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. 13% 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; 374 lines (11%) are > 80 characters long.
First few lines:
• R/AllClasses.R#L6 #' @slot analysis A data.frame containin ...
• ...
• vignettes/damidBind_vignette.Rmd#L341 Below are the first 20 lines of
`analysi ...
i NOTE: Consider multiples of 4 spaces for line indents; 5 lines (0%) are not.
First few lines:
• R/plot_venn.R#L136 venn <- do.call(BioVenn::draw ...
• ...
• damidBind/NAMESPACE#L7 theme, theme_bw) ...
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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the damidBind.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.