===============================
BiocCheckGitClone('HiCaptuRe')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/e3a7d86c9b798409772408b94e7417db09e97197/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/e3a7d86c9b798409772408b94e7417db09e97197/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/e3a7d86c9b798409772408b94e7417db09e97197/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/e3a7d86c9b798409772408b94e7417db09e97197/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 ‘0.99.2’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
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.
* 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 ... WARNING
Found the following file with non-ASCII characters:
R/HiCaptuRe-class.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [19s/19s] OK
* checking whether the package can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the package can be unloaded cleanly ... [18s/18s] OK
* checking whether the namespace can be loaded with stated dependencies ... [18s/18s] OK
* checking whether the namespace can be unloaded cleanly ... [18s/18s] OK
* checking loading without being on the library search path ... [17s/17s] OK
* checking whether startup messages can be suppressed ... [18s/18s] 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 ... [55s/55s] 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 'getters.Rd':
\examples lines wider than 100 characters:
regions <- GenomicRanges::GRanges(seqnames = 19, ranges = 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(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 ... [28s/28s] ERROR
Running examples in ‘HiCaptuRe-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: export_interactions
> ### Title: Export interactions in the desired output format
> ### Aliases: export_interactions
>
> ### ** Examples
>
> export_interactions(interactions, file = "output.ibed", format = "ibed", over.write = TRUE)
Error in h(simpleError(msg, call)) :
error in evaluating the argument 'x' in selecting a method for function 'getParameters': object 'interactions' not found
Calls: export_interactions -> getParameters -> .handleSimpleError -> h
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [57s/57s]
[57s/57s] 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3865/e3a7d86c9b798409772408b94e7417db09e97197/HiCaptuRe.Rcheck/00check.log’
for details.
===============================
BiocCheck('HiCaptuRe_0.99.2.tar.gz')
===============================
── Installing HiCaptuRe ────────────────────────────────────────────────────────
✔ Package installed successfully
── HiCaptuRe session metadata ──────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpwkFUPw/file3d142a3ccb4910/HiCaptuRe
→ BiocVersion: 3.22
→ Package: HiCaptuRe
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3865/e3a7d86c9b798409772408b94e7417db09e97197/HiCaptuRe.BiocCheck
→ BiocCheckVersion: 1.45.8
→ sourceDir: /tmp/RtmpwkFUPw/file3d142a3ccb4910/HiCaptuRe
→ installDir: /tmp/RtmpwkFUPw/file3d142a6ca916a4
→ 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.