===============================
R CMD BUILD
===============================
* 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_0.99.7.tar.gz
===============================
BiocCheckGitClone('looplook')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/a2079de801a915200070beb40200979579a44288/looplook
BiocVersion: 3.23
Package: looplook
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/a2079de801a915200070beb40200979579a44288/looplook.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/a2079de801a915200070beb40200979579a44288/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 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 v1.47.20 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/a2079de801a915200070beb40200979579a44288/looplook.Rcheck
* using R Under development (unstable) (2026-03-05 r89546)
* 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 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-03-25 11:47:33 UTC
* using option --no-vignettes
* checking for file looplook/DESCRIPTION ... OK
* this is package looplook version 0.99.7
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ... [14s/14s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [13s/13s] OK
* checking whether the namespace can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] OK
* checking loading without being on the library search path ... [14s/14s] 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 ... [49s/49s] 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 ... [144s/144s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
annotate_peaks_and_loops 87.868 1.733 89.608
plot_peaks_interactions 17.657 0.796 18.453
refine_loop_anchors_by_expression 4.947 0.041 5.002
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [58s/58s]
[58s/58s] 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: OK
===============================
BiocCheck('looplook_0.99.7.tar.gz')
===============================
Installing looplook
Package installed successfully
looplook session metadata
sourceDir: /tmp/RtmpwoPuL7/file1cd8e72f32fc0b/looplook
BiocVersion: 3.23
Package: looplook
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/a2079de801a915200070beb40200979579a44288/looplook.BiocCheck
BiocCheckVersion: 1.47.20
sourceDir: /tmp/RtmpwoPuL7/file1cd8e72f32fc0b/looplook
installDir: /tmp/RtmpwoPuL7/file1cd8e74742e625
isTarBall: TRUE
platform: unix
Running BiocCheck on looplook
* Checking for deprecated package usage...
Error while performing HEAD request.
Proceeding without cache information.
Error in if (identical(nrow(bquery), 1L) && bfcneedsupdate(bfc, bquery[["rid"]])) bfcdownload(x = bfc, :
missing value where TRUE/FALSE needed
Calls: BiocCheck ... getAllDeprecatedPkgs -> get_deprecated_status -> get_status_file_cache
Execution halted