===============================
R CMD BUILD
===============================
* checking for file ‘proBatch/DESCRIPTION’ ... OK
* preparing ‘proBatch’:
* checking DESCRIPTION meta-information ... OK
* installing the package 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
* looking to see if a ‘data/datalist’ file should be added
* building ‘proBatch_1.99.3.tar.gz’
===============================
BiocCheckGitClone('proBatch')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch
→ BiocVersion: 3.22
→ Package: proBatch
→ PackageVersion: 1.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch
→ 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...
* Checking that provided CITATION file is correctly formatted...
── BiocCheck v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘proBatch/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘proBatch’ version ‘1.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 29 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 ‘proBatch’ 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 ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [11s/11s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the namespace can be unloaded cleanly ... [11s/11s] OK
* checking loading without being on the library search path ... [11s/11s] OK
* checking whether startup messages can be suppressed ... [11s/11s] 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 ... [42s/42s] OK
* checking Rd files ... [1s/1s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [1s/1s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [204s/204s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plot_PVCA 34.301 0.192 34.494
plot_PVCA.df 16.917 0.046 16.963
calculate_PVCA 16.800 0.081 16.881
prepare_PVCA_df 16.862 0.016 16.879
feature_level_diagnostics 12.225 0.043 12.269
correct_batch_effects 8.104 0.024 8.129
plot_sample_mean_or_boxplot 7.499 0.098 7.598
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’ [0s/0s]
Running ‘testthat.R’ [71s/72s]
[72s/72s] 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 ... [6s/6s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('proBatch_1.99.3.tar.gz')
===============================
── Installing proBatch ─────────────────────────────────────────────────────────
✔ Package installed successfully
── proBatch session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpdnHTGq/file18099adc74685/proBatch
→ BiocVersion: 3.22
→ Package: proBatch
→ PackageVersion: 1.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3975/proBatch_20251021073505/proBatch.BiocCheck
→ BiocCheckVersion: 1.45.20
→ sourceDir: /tmp/RtmpdnHTGq/file18099adc74685/proBatch
→ installDir: /tmp/RtmpdnHTGq/file18099a5bd1938e
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on proBatch ───────────────────────────────────────────────
* 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...
! WARNING: New package x version starting with non-zero value (e.g., 1.y.z,
2.y.z); got ‘1.99.3’.
* Checking R version dependency...
* 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: GeneExpression
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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (24%).
* 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 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 proBatch...
* 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 49
functions greater than 50 lines.
The longest 5 functions are:
• plot_single_feature() (R/feature_level_diagnostics.R): 204 lines
• ...
• pb_add_level() (R/ProBatchFeatures.R): 145 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• convert_annotation_classes.Rd
• ...
• warn_unmapped_columns.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; 524 lines (4%) are > 80 characters long.
First few lines:
• R/auxiliary.R#L91 message("Checking sample consist ...
• ...
• vignettes/proBatchFeatures.Rmd#L668 ```{r plot_pvca_panels, fig.height=6, fi
...
i NOTE: Consider multiples of 4 spaces for line indents; 619 lines (5%) are
not.
First few lines:
• R/auxiliary.R#L18 feature_id_co ...
• ...
• R/utility_funcs.R#L399 minimal_col ...
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 v1.45.20 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 7 NOTES
i See the proBatch.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.