===============================
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_0.99.16.tar.gz’
===============================
BiocCheckGitClone('looplook')
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── Running Git clone checks on looplook ────────────────────────────────────────
* Checking valid files...
* Checking for inst/doc folders...
* Checking DESCRIPTION readability...
* Checking for valid use of maintainer fields...
===============================
R CMD CHECK
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* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/4151/ba65aea788f13443ee26c418bd3bc66069aa7200/looplook.Rcheck’
* using R version 4.6.1 (2026-06-24)
* 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: 2026-08-11 11:21:01 UTC
* using option ‘--no-vignettes’
* checking for file ‘looplook/DESCRIPTION’ ... OK
* this is package ‘looplook’ version ‘0.99.16’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ... INFO
installed size is 5.1Mb
sub-directories of 1Mb or more:
extdata 1.4Mb
help 2.8Mb
* 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 ... [15s/15s] 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 ... [15s/15s] OK
* checking loading without being on the library search path ... [15s/15s] 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 ... [61s/61s] 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 ... [83s/83s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
looplook_report 21.415 0.901 21.798
annotate_peaks_and_loops 11.074 0.595 11.663
refine_loop_anchors_by_expression 6.348 0.269 6.617
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('looplook_0.99.16.tar.gz')
===============================
── Installing looplook ─────────────────────────────────────────────────────────
✔ Package installed successfully
── looplook session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpE60gCC/file3d7ee76cb45af7/looplook
→ BiocVersion: 3.23
→ Package: looplook
→ PackageVersion: 0.99.16
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4151/ba65aea788f13443ee26c418bd3bc66069aa7200/looplook.BiocCheck
→ BiocCheckVersion: 1.49.30
→ sourceDir: /tmp/RtmpE60gCC/file3d7ee76cb45af7/looplook
→ installDir: /tmp/RtmpE60gCC/file3d7ee71a2828be/lib
→ 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: Transcription,
LongRead, ChipOnChip, AnnotationHubSoftware, ExperimentHubSoftware,
GenomeAssembly, MotifAnnotation, PeakDetection, ExperimentalDesign,
MultipleComparison, KEGG, GraphAndNetwork
i Search 'biocViews' at https://contributions.bioconductor.org
* Checking build system compatibility...
* Checking if 'Package:' field matches directory / tarball...
* Checking for Version: field...
* Checking DESCRIPTION readability...
* Checking validity of DESCRIPTION fields...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for whitespace in DESCRIPTION field names...
* Checking for proper Description: field...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (38%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
* 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...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/data_processing.R (line 1236, column 11)
• R/utils.R (line 1721, column 12)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 19 times)
• suppressWarnings() in R/analysis.R (line 979, column 16)
• ...
• suppressMessages() in R/utils.R (line 2118, column 9)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 94
functions greater than 50 lines.
The longest 5 functions are:
• refine_loop_anchors_by_chromatin() (R/annotation.R): 350 lines
• ...
• .chromatin_post_reclassify() (R/annotation.R): 320 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; 1340 lines (7%) are > 80 characters long.
First few lines:
• R/analysis.R#L4 #' Integrates 3D genomic interaction dat ...
• ...
• vignettes/looplook.Rmd#L1456 **Solution:** Either render via `ggsave( ...
i NOTE: Consider multiples of 4 spaces for line indents; 7962 lines (40%) are
not.
First few lines:
• R/analysis.R#L156 annotation_res, ...
• ...
• vignettes/looplook.Rmd#L1121 print(track_plot) ...
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 'looplook' is already in your 'Watched Tags' on the Support Site.
── BiocCheck v1.49.30 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 7 NOTES
i See the looplook.BiocCheck folder and run
`browseVignettes(package = 'BiocCheck')`
for details.