===============================
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
* building ‘HiCaptuRe_0.99.12.tar.gz’
===============================
BiocCheckGitClone('HiCaptuRe')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/704ef62710a0d29dc5348c59730c6efe426dced7/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.12
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/704ef62710a0d29dc5348c59730c6efe426dced7/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/704ef62710a0d29dc5348c59730c6efe426dced7/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 v1.45.12 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/3865/704ef62710a0d29dc5348c59730c6efe426dced7/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 ‘0.99.12’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 22 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 ‘HiCaptuRe’ 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [14s/14s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking whether startup messages can be suppressed ... [15s/15s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: 'magrittr'
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [46s/46s] NOTE
interactionsByBaits: no visible binding for global variable 'bait'
Undefined global functions or variables:
bait
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'export_interactions.Rd':
\examples lines wider than 100 characters:
export_interactions(interactions = interactions, file = tempfile(), format = "ibed", over.write = TRUE)
Rd file 'getters.Rd':
\examples lines wider than 100 characters:
regions <- GenomicRanges::GRanges(seqnames = 19, ranges = IRanges::IRanges(start = c(500000, 1000000), end = c(510000, 1100000)))
Rd file 'interactionsByRegions.Rd':
\examples lines wider than 100 characters:
regions <- GenomicRanges::GRanges(seqnames = 19, ranges = IRanges::IRanges(start = c(500000, 1000000), end = c(510000, 1100000)))
These lines will be truncated in the PDF manual.
* 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 ... [36s/36s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [26s/26s]
[26s/26s] ERROR
Running the tests in ‘tests/testthat.R’ failed.
Last 20 lines of output:
> library(testthat)
> library(HiCaptuRe)
── Attaching HiCaptuRe package ────────────────────────────── version 0.99.12 ──
i Please report any bug or ask for a feature in our GitHub (<https://github.com/LaureTomas/HiCaptuRe>)
>
> test_check("HiCaptuRe")
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 65 ]
══ Failed tests ════════════════════════════════════════════════════════════════
── Failure ('test-digest_genome.R:7:5'): digest_genome returns GRanges fragments ──
class(digest$digest) not equal to "data.frame".
Lengths differ: 2 is not 1
── Error ('test-export_interactions.R:52:5'): export_interactions: bedpe exports empty file when all rows filtered out ──
Error in `setup_load_chr19()`: could not find function "setup_load_chr19"
── Error ('test-export_interactions.R:64:5'): export_interactions: seqmonk duplicates anchors and drops ID column in file ──
Error in `setup_load_chr19()`: could not find function "setup_load_chr19"
[ FAIL 3 | WARN 0 | SKIP 0 | PASS 65 ]
Error: Test failures
Execution halted
* 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: 1 ERROR, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3865/704ef62710a0d29dc5348c59730c6efe426dced7/HiCaptuRe.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCaptuRe_0.99.12.tar.gz')
===============================
── Installing HiCaptuRe ────────────────────────────────────────────────────────
✔ Package installed successfully
── HiCaptuRe session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp9kOguP/file2af3f1fb00ec0/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.12
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/704ef62710a0d29dc5348c59730c6efe426dced7/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.12
→ sourceDir: /tmp/Rtmp9kOguP/file2af3f1fb00ec0/HiCaptuRe
→ installDir: /tmp/Rtmp9kOguP/file2af3f2aeb6cd8
→ 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...
* 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 (33%).
* 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 1:...; use seq_len() or seq_along()
Found in files:
• load_interactions.R (line 67, column 53)
• ...
• load_interactions.R (line 311, column 75)
* 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 14 times)
• suppressMessages() in R/annotate_interactions.R (line 48, column 9)
• ...
• suppressWarnings() in R/intersect_interactions.R (line 110, 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...
* 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; 399 lines (15%) are > 80 characters long.
First few lines:
• R/annotate_interactions.R#L3 #' This function annotate a HiCaptuRe ob ...
• ...
• vignettes/vignetteIntroduction.Rmd#L350 - Tomás-Daza, L., Rovirosa, L. *et
al.* ...
i NOTE: Consider multiples of 4 spaces for line indents; 61 lines (2%) are not.
First few lines:
• vignettes/vignette_functions.Rmd#L515 - A single peakmatrix file using `form
...
• ...
• vignettes/vignetteIntroduction.Rmd#L332 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 v1.45.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the HiCaptuRe.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.