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R CMD BUILD
===============================
* checking for file ‘barbieQ/DESCRIPTION’ ... OK
* preparing ‘barbieQ’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘barbieQ_0.99.0.tar.gz’
===============================
BiocCheckGitClone('barbieQ')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3747/barbieQ_20250224152646/barbieQ
→ BiocVersion: 3.21
→ Package: barbieQ
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3747/barbieQ_20250224152646/barbieQ.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3747/barbieQ_20250224152646/barbieQ
→ 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 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 v1.43.12 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/3747/barbieQ_20250224152646/barbieQ.Rcheck’
* using R Under development (unstable) (2025-02-19 r87757)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘barbieQ/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barbieQ’ version ‘0.99.0’
* 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 ... NOTE
Found the following hidden files and directories:
.github
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘barbieQ’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* 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 ... [4s/4s] OK
* checking whether the package can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [4s/4s] OK
* checking whether the namespace can be unloaded cleanly ... [4s/4s] OK
* checking loading without being on the library search path ... [5s/5s] 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 ... [16s/16s] NOTE
extractBarcodePairs: no visible binding for global variable ‘p.value’
extractBarcodePairs: no visible binding for global variable
‘adj.p.value’
plotBarcodeBiasScatterPlot: no visible binding for global variable
‘minusLogP’
plotBarcodeBiasScatterPlot: no visible binding for global variable
‘BarcodeID’
plotBarcodeBiasScatterPlot: no visible binding for global variable
‘direction’
plotBarcodePairCorrelation: no visible binding for global variable
‘count’
plotBarcodePairCorrelation: no visible binding for global variable
‘knownCorrelating’
plotBarcodePairCorrelation: no visible binding for global variable
‘..y..’
plotBarcodePareto: no visible binding for global variable ‘group’
plotBarcodePareto: no visible binding for global variable ‘value’
plotBarcodePareto: no visible binding for global variable ‘id’
plotBarcodeProportion: no visible binding for global variable
‘percentage’
plotBarcodeSankey: no visible binding for global variable ‘category’
plotBarcodeSankey: no visible binding for global variable ‘value’
plotBarcodeSankey: no visible binding for global variable ‘variable’
plotSamplePairCorrelation: no visible binding for global variable
‘rowNumber’
Undefined global functions or variables:
..y.. BarcodeID adj.p.value category count direction group id
knownCorrelating minusLogP p.value percentage rowNumber value
variable
* 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 ... [26s/26s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotBarcodePairCorrelation 5.596 0.026 5.622
clusterCorrelatingBarcodes 4.960 0.089 5.049
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [25s/25s]
[25s/25s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3747/barbieQ_20250224152646/barbieQ.Rcheck/00check.log’
for details.
===============================
BiocCheck('barbieQ_0.99.0.tar.gz')
===============================
── Installing barbieQ ──────────────────────────────────────────────────────────
✔ Package installed successfully
── barbieQ session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp3ilfPU/file32e90f27eade/barbieQ
→ BiocVersion: 3.21
→ Package: barbieQ
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3747/barbieQ_20250224152646/barbieQ.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/Rtmp3ilfPU/file32e90f27eade/barbieQ
→ installDir: /tmp/Rtmp3ilfPU/file32e90f63abaa6d
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on barbieQ ────────────────────────────────────────────────
* 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...
* 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...
* 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 (15%).
* 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 .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 barbieQ...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 3 times)
• suppressWarnings() in R/BarcodePairCorrelation.R (line 60, column 3)
• suppressWarnings() in R/plotBarcodePareto.R (line 96, column 3)
• suppressWarnings() in R/plotBarcodeProportion.R (line 66, column 3)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 17
functions greater than 50 lines.
The longest 5 functions are:
• testBarcodeBias() (R/testBarcodeBias.R): 208 lines
• ...
• plotBarcodeBiasScatterPlot() (R/plotBarcodeBias.R): 82 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; 184 lines (6%) are > 80 characters long.
First few lines:
• R/BarcodePairCorrelation.R#L59 ## ggplot2 has a bug that gives wrong ...
• ...
• vignettes/barbieQ.Rmd#L186 We are currently writing a paper to intr ...
i NOTE: Consider multiples of 4 spaces for line indents; 1052 lines (34%) are
not.
First few lines:
• R/BarcodePairCorrelation.R#L44 ## check dataVisual ...
• ...
• vignettes/barbieQ.Rmd#L178 method = "diffOcc" ...
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 v1.43.12 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 5 NOTES
i See the barbieQ.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.