===============================
R CMD BUILD
===============================
* checking for file ‘HiCaptuRe/DESCRIPTION’ ... OK
* preparing ‘HiCaptuRe’:
* 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
NB: this package now depends on R (>= 4.1.0)
WARNING: Added dependency on R >= 4.1.0 because package code uses the
pipe |> or function shorthand \(...) syntax added in R 4.1.0.
File(s) using such syntax:
‘distance_summary.R’ ‘export_interactions.R’ ‘interactionsByBaits.R’
‘interactionsByRegions.R’ ‘intersect_interactions.R’
‘load_interactions.R’
* building ‘HiCaptuRe_0.99.1.tar.gz’
===============================
BiocCheckGitClone('HiCaptuRe')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe
→ 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 v1.45.8 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/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe.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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HiCaptuRe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HiCaptuRe’ version ‘0.99.1’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... ERROR
Namespace dependency missing from DESCRIPTION Imports/Depends entries: ‘progressr’
Imports includes 21 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.
See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCaptuRe_0.99.1.tar.gz')
===============================
── Installing HiCaptuRe ────────────────────────────────────────────────────────
✔ Package installed successfully
── HiCaptuRe session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpu3Ve23/file3939645753f30f/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/b0b95351bc9d4a8c9de33781881349c3fdc5b5d8/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /tmp/Rtmpu3Ve23/file3939645753f30f/HiCaptuRe
→ installDir: /tmp/Rtmpu3Ve23/file3939641cf12876
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on HiCaptuRe ──────────────────────────────────────────────
* 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 4.1.0 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 (30%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• vignette_functions.Rmd
• vignetteIntroduction.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of HiCaptuRe...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/interactionsByBaits.R (line 24, column 12)
• R/interactionsByBaits.R (line 25, column 12)
• R/intersect_interactions.R (line 36, column 26)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• digest_genome.R (line 31, column 117)
• ...
• peakmatrix2list.R (line 34, column 56)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
• R/digest_genome.R (line 82, column 22)
• R/load_interactions.R (line 26, column 14)
• R/peakmatrix2list.R (line 22, column 14)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid '<<-' if possible (found 1 times)
• <<- in R/zzz.R (line 9, column 19)
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 15 times)
• suppressMessages() in R/annotate_interactions.R (line 47, column 9)
• ...
• suppressWarnings() in R/intersect_interactions.R (line 109, column 18)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
The longest 5 functions are:
• interactionsByRegions() (R/interactionsByRegions.R): 163 lines
• ...
• interactionsByBaits() (R/interactionsByBaits.R): 67 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 393 lines (15%) are > 80 characters long.
First few lines:
• R/annotate_interactions.R#L3 #' This function annotate a HiCaptuRe ob ...
• ...
• vignettes/vignetteIntroduction.Rmd#L324 - Tomás-Daza, L., Rovirosa, L. *et
al.* ...
i NOTE: Consider multiples of 4 spaces for line indents; 62 lines (2%) are not.
First few lines:
• R/load_interactions.R#L103 stop("Could not detect a valid for ...
• ...
• vignettes/vignetteIntroduction.Rmd#L306 A tab-delimited file with bait
annotat ...
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 v1.45.8 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 12 NOTES
i See the HiCaptuRe.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.