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R CMD BUILD
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* checking for file looplook/DESCRIPTION ... OK
* preparing looplook:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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 looplook_0.99.9.tar.gz
===============================
BiocCheckGitClone('looplook')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/b33ac445533c5e4906eb8621e6f9a764ea1de42c/looplook
BiocVersion: 3.23
Package: looplook
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/b33ac445533c5e4906eb8621e6f9a764ea1de42c/looplook.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/b33ac445533c5e4906eb8621e6f9a764ea1de42c/looplook
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 remote package usage...
* 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 v1.49.4 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/4151/b33ac445533c5e4906eb8621e6f9a764ea1de42c/looplook.Rcheck
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-11 08:33:27 UTC
* using option --no-vignettes
* checking for file looplook/DESCRIPTION ... OK
* this is package looplook version 0.99.9
* 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 looplook 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 ... [30s/36s] OK
* checking whether the package can be loaded with stated dependencies ... [21s/22s] OK
* checking whether the package can be unloaded cleanly ... [20s/20s] 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 ... [28s/31s] 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 ... [63s/63s] 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 ... [221s/221s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_peaks_and_loops 103.858 2.336 106.198
looplook_report 37.791 1.030 38.779
plot_peaks_interactions 21.933 1.153 23.089
refine_loop_anchors_by_expression 9.079 0.264 9.346
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('looplook_0.99.9.tar.gz')
===============================
Installing looplook
Package installed successfully
looplook session metadata
sourceDir: /tmp/Rtmp9y9Ak2/filef4b01126d2356/looplook
BiocVersion: 3.23
Package: looplook
PackageVersion: 0.99.9
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/b33ac445533c5e4906eb8621e6f9a764ea1de42c/looplook.BiocCheck
BiocCheckVersion: 1.49.4
sourceDir: /tmp/Rtmp9y9Ak2/filef4b01126d2356/looplook
installDir: /tmp/Rtmp9y9Ak2/filef4b0165005f83
isTarBall: TRUE
platform: unix
Running BiocCheck on looplook
* 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 4.5.0 to 4.6.0
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
AnnotationHubSoftware, GenomeAssembly, MotifAnnotation, PeakDetection, KEGG
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking for proper Description: field...
* Checking if DESCRIPTION is well formatted...
* Checking for whitespace in DESCRIPTION field names...
* Checking if 'Package:' field matches directory / tarball...
* 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 (36%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 looplook...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 25
functions greater than 50 lines.
The longest 5 functions are:
annotate_peaks_and_loops() (R/annotation.R): 446 lines
...
compute_refined_stats() (R/utils.R): 223 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/print.looplook_karyo.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; 783 lines (12%) are > 80 characters long.
First few lines:
R/analysis.R#L4 #' Integrates 3D genomic interaction dat ...
...
vignettes/looplook.Rmd#L814 The template is also accessible from the ...
i NOTE: Consider multiples of 4 spaces for line indents; 2427 lines (36%) are
not.
First few lines:
R/analysis.R#L70 annotation_res, ...
...
vignettes/looplook.Rmd#L810 run_go = TRUE ...
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 v1.49.4 results
0 ERRORS | 1 WARNINGS | i 5 NOTES
i See the looplook.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.