===============================
R CMD BUILD
===============================
* checking for file ‘fourSynergy/DESCRIPTION’ ... OK
* preparing ‘fourSynergy’:
* 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 ‘fourSynergy_0.99.2.tar.gz’
===============================
BiocCheckGitClone('fourSynergy')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3992/6403b50cba5b49d8b137ec32c955ef7f007d1525/fourSynergy
→ BiocVersion: 3.23
→ Package: fourSynergy
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3992/6403b50cba5b49d8b137ec32c955ef7f007d1525/fourSynergy.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3992/6403b50cba5b49d8b137ec32c955ef7f007d1525/fourSynergy
→ 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 v1.47.7 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/3992/6403b50cba5b49d8b137ec32c955ef7f007d1525/fourSynergy.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 24.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘fourSynergy/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘fourSynergy’ version ‘0.99.2’
* 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 ‘fourSynergy’ can be installed ... OK
* checking installed package size ... INFO
installed size is 5.8Mb
sub-directories of 1Mb or more:
extdata 5.6Mb
* 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 ... [15s/15s] OK
* checking whether the package can be unloaded cleanly ... [15s/15s] 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 ... [46s/46s] 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 ... [121s/121s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotIaIndiviualTools 28.253 0.344 28.599
plotDiffIa 12.958 0.154 13.112
differentialAnalysis 11.307 0.163 11.471
plotConsensusTracks 10.823 0.150 10.975
plotConsensusIa 10.813 0.121 10.935
consensusIa 9.765 0.281 10.479
plotBaseTracks 7.395 0.099 7.496
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [117s/118s]
[118s/118s] 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 ... [3s/3s] OK
* DONE
Status: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('fourSynergy_0.99.2.tar.gz')
===============================
── Installing fourSynergy ──────────────────────────────────────────────────────
✔ Package installed successfully
── fourSynergy session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpRqzZhU/file16aa251697f26c/fourSynergy
→ BiocVersion: 3.23
→ Package: fourSynergy
→ PackageVersion: 0.99.2
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3992/6403b50cba5b49d8b137ec32c955ef7f007d1525/fourSynergy.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/RtmpRqzZhU/file16aa251697f26c/fourSynergy
→ installDir: /tmp/RtmpRqzZhU/file16aa2561da7ecd
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on fourSynergy ────────────────────────────────────────────
* 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: Coverage
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 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 (29%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
• fourSynergy_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of fourSynergy...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/utils.R (line 141, column 18)
• R/utils.R (line 169, column 14)
• R/utils.R (line 173, column 29)
* 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 11
functions greater than 50 lines.
The longest 5 functions are:
• consensusIa() (R/consensusIa.R): 168 lines
• ...
• differentialAnalysis() (R/differentialAnalysis.R): 97 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• setDds.Rd
• setDifferential.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; 8 lines (0%) are > 80 characters long.
First few lines:
• R/plotBaseTracks.R#L50 mcols(res$tmp[queryHits(ov)])[[p ...
• ...
• R/utils.R#L173 is_valid_seq <- all(sapply(confi ...
i NOTE: Consider multiples of 4 spaces for line indents; 16 lines (1%) are not.
First few lines:
• R/AllGenerics.R#L84 hi ...
• ...
• R/plotIaIndividualTools.R#L119 cex = cex.leg) ...
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 v1.47.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the fourSynergy.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.