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R CMD BUILD
===============================
* checking for file PloidyPeaks/DESCRIPTION ... OK
* preparing PloidyPeaks:
* 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
WARNING: Removing directory PloidyPeaks/Meta which should only occur
in an installed package
* building PloidyPeaks_0.99.13.tar.gz
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BiocCheckGitClone('PloidyPeaks')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks
BiocVersion: 3.23
Package: PloidyPeaks
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks
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 v1.47.18 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/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* 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 PloidyPeaks/DESCRIPTION ... OK
* this is package PloidyPeaks version 0.99.13
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 25 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 serialization versions ... OK
* checking whether package PloidyPeaks can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import data.table::first by dplyr::first when loading PloidyPeaks
Warning: replacing previous import data.table::between by dplyr::between when loading PloidyPeaks
Warning: replacing previous import data.table::last by dplyr::last when loading PloidyPeaks
Warning: replacing previous import dplyr::combine by gridExtra::combine when loading PloidyPeaks
Warning: replacing previous import cowplot::align_plots by patchwork::align_plots when loading PloidyPeaks
Warning: replacing previous import dplyr::data_frame by vctrs::data_frame when loading PloidyPeaks
See /home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks.Rcheck/00install.out for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking build directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
ggplot2
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... NOTE
Found the following CITATION file in a non-standard place:
CITATION
Most likely inst/CITATION should be used instead.
Problems with news in NEWS.md:
No news entries found.
* 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 ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] 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 ... [4s/4s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespaces in Imports field not imported from:
AzureRMR AzureStor BiocFileCache here htmltools
kableExtra
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [25s/25s] NOTE
.createPDF: no visible global function definition for pdf
.outputData: no visible binding for global variable G1_3
.plotSamples: no visible binding for global variable x
.plotSamples: no visible binding for global variable y
RSEOutlierDetection: no visible global function definition for
read.csv
RSEOutlierDetection: no visible binding for global variable finalRSE
RSEOutlierDetection: no visible binding for global variable dnorm
RSEOutlierDetection: no visible global function definition for sd
RSEOutlierDetection: no visible global function definition for median
massFlowGraph: no visible global function definition for read.csv
massFlowGraph: no visible global function definition for menu
Undefined global functions or variables:
G1_3 dnorm finalRSE median menu pdf read.csv sd x y
Consider adding
importFrom("grDevices", "pdf")
importFrom("stats", "dnorm", "median", "sd")
importFrom("utils", "menu", "read.csv")
to your NAMESPACE file.
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'RSEOutlierDetection.Rd':
\examples lines wider than 100 characters:
csv <- "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/analysis/ploidyPeaksOutput.csv"
Rd file 'massFlowGraph.Rd':
\examples lines wider than 100 characters:
csv <- "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/analysis/ploidyPeaksOutput.csv"
Rd file 'peakCorrection.Rd':
\examples lines wider than 100 characters:
urls <- c("https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_4.fcs")
Rd file 'rectGateFlowFrame.Rd':
\examples lines wider than 100 characters:
urls <- c("https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_1.fcs")
These lines will be truncated in the PDF manual.
* 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 ... [28s/33s] WARNING
Found the following significant warnings:
Warning: working directory was changed to /tmp/RtmpLG2FwU/bioc_cache_3e9a884db9e6b3/fcs_data, resetting
Warning: working directory was changed to /tmp/RtmpLG2FwU/bioc_cache_3e9a88e82474f/fcs_data, resetting
Warning: working directory was changed to /tmp/RtmpLG2FwU/bioc_cache_3e9a8831a27329/fcs_data, resetting
Warning: working directory was changed to /tmp/RtmpLG2FwU/bioc_cache_3e9a88ceb7e8e/fcs_data, resetting
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
RSEOutlierDetection 4.440 0.801 6.746
flowLineGraph 4.018 0.629 5.617
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [4s/4s]
[4s/4s] 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: 2 WARNINGs, 5 NOTEs
See
/home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks.Rcheck/00check.log
for details.
===============================
BiocCheck('PloidyPeaks_0.99.13.tar.gz')
===============================
Installing PloidyPeaks
Package installed successfully
PloidyPeaks session metadata
sourceDir: /tmp/Rtmpj7khUM/file3e9c427e376e5f/PloidyPeaks
BiocVersion: 3.23
Package: PloidyPeaks
PackageVersion: 0.99.13
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/0de88e70a07eb974c34cec80c96f10572040a942/PloidyPeaks.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/Rtmpj7khUM/file3e9c427e376e5f/PloidyPeaks
installDir: /tmp/Rtmpj7khUM/file3e9c426f248c58
isTarBall: TRUE
platform: unix
Running BiocCheck on PloidyPeaks
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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...
i NOTE: Provide 'URL' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (14%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
Found in files:
ploidyPeaks.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of PloidyPeaks...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/flowLineGraph.R (line 120, column 24)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
flowLineGraph.R (line 734, column 15)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
cat() in R/flowLineGraph.R (line 744, column 7)
...
print() in R/RSEOutlierDetection.R (line 151, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
R/flowLineGraph.R (line 96, column 15)
...
R/RSEOutlierDetection.R (line 86, column 21)
* 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 26
functions greater than 50 lines.
The longest 5 functions are:
.outputData() (R/flowPeakDetection.R): 1240 lines
...
.popConfidence3Pop() (R/flowPeakDetection.R): 482 lines
* Checking man page documentation...
Warning: replacing previous import data.table::first by dplyr::first when loading PloidyPeaks
Warning: replacing previous import data.table::between by dplyr::between when loading PloidyPeaks
Warning: replacing previous import data.table::last by dplyr::last when loading PloidyPeaks
Warning: replacing previous import dplyr::combine by gridExtra::combine when loading PloidyPeaks
Warning: replacing previous import cowplot::align_plots by patchwork::align_plots when loading PloidyPeaks
Warning: replacing previous import dplyr::data_frame by vctrs::data_frame when loading PloidyPeaks
* Checking package NEWS...
! WARNING: news(package='PloidyPeaks') failed with news file:
PloidyPeaks/NEWS.md:news() failed to parse news file: PloidyPeaks/NEWS.md Refer
to https://contributions.bioconductor.org/news.html to be included in
Bioconductor release announcements.
* 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; 175 lines (2%) are > 80 characters long.
First few lines:
R/flowLineGraph.R#L26 #' grid where the first entry is the la ...
...
vignettes/ploidyPeaks.Rmd#L492 Now, we can look at the *.csv* files, pl ...
i NOTE: Consider multiples of 4 spaces for line indents; 2743 lines (26%) are
not.
First few lines:
R/flowLineGraph.R#L112 getwd() ...
...
vignettes/ploidyPeaks.Rmd#L476 fileName = "allSamples" ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/experiment
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/workflows/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/workflows
* 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 v1.47.18 results
0 ERRORS | 1 WARNINGS | i 11 NOTES
i See the PloidyPeaks.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.