===============================
BiocCheckGitClone('PloidyPeaks')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/PloidyPeaks
→ BiocVersion: 3.21
→ Package: PloidyPeaks
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/PloidyPeaks.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/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 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/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/PloidyPeaks.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 ‘PloidyPeaks/DESCRIPTION’ ... OK
* this is package ‘PloidyPeaks’ version ‘0.99.10’
* 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::last’ by ‘dplyr::last’ when loading ‘PloidyPeaks’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ 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/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/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 ... OK
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] OK
* checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] 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 ... [20s/20s] 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 ... [7s/9s] ERROR
Running examples in ‘PloidyPeaks-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RSEOutlierDetection
> ### Title: RSEOutlierDetection
> ### Aliases: RSEOutlierDetection
>
> ### ** Examples
>
> library(BiocFileCache)
Loading required package: dbplyr
> original_wd <- getwd()
> cachePath <- tempfile(pattern = "bioc_cache_")
> dir.create(cachePath, showWarnings = FALSE)
> bfc <- BiocFileCache(cachePath, ask = FALSE)
> on.exit({
+ if(normalizePath(cachePath) == normalizePath(getwd())){
+ setwd(tempdir())
+ }
+ unlink(cachePath, recursive = TRUE, force = TRUE)
+ }, add = TRUE)
> gatedFolder <- file.path(cachePath, "fcs_data")
> dir.create(gatedFolder, showWarnings = FALSE)
> urls <- c(
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_1.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_2.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_3.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_4.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_5.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_6.fcs"
+ )
> rids <- vapply(urls, function(url){
+ res <- bfcquery(bfc, url)
+ if(nrow(res) == 0){
+ bfcadd(bfc, basename(url), url)
+ }else{
+ res$rid[1]
+ }
+ }, character(1))
> fpaths <- bfcrpath(bfc, urls)
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_1.fcs'
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_2.fcs'
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_3.fcs'
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_4.fcs'
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_5.fcs'
adding rname 'https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/gated_data/A1_6.fcs'
> newFPaths <- file.path(gatedFolder, basename(urls))
> file.copy(fpaths, newFPaths, overwrite = TRUE)
[1] TRUE TRUE TRUE TRUE TRUE TRUE
> downloadedFiles <- newFPaths
> csv <- "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/analysis/ploidyPeaksOutput.csv"
> rid <- bfcquery(bfc, csv, field = "rname")$rid
> if (length(rid) == 0) {
+ rid <- bfcadd(bfc, csv, csv)
+ }
> cachedFile <- bfcrpath(bfc, rid)
adding rname '/tmp/RtmpBSCx2D/bioc_cache_113e603caf96d4/113e607bd70b7f_ploidyPeaksOutput.csv'
> analysisFile <- file.path(csvFolder, basename(csv))
Error: object 'csvFolder' not found
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[3s/3s] 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: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/PloidyPeaks.Rcheck/00check.log’
for details.
===============================
BiocCheck('PloidyPeaks_0.99.10.tar.gz')
===============================
── Installing PloidyPeaks ──────────────────────────────────────────────────────
✔ Package installed successfully
── PloidyPeaks session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmpdqcc8s/file1140114545b26b/PloidyPeaks
→ BiocVersion: 3.21
→ Package: PloidyPeaks
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3567/28bc07b97b1da1aa1b9a4d6034c56ae71209fe3a/PloidyPeaks.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/Rtmpdqcc8s/file1140114545b26b/PloidyPeaks
→ installDir: /tmp/Rtmpdqcc8s/file1140116860e0dd
→ 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...
* 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 (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 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): 480 lines
* Checking man page documentation...
Warning: replacing previous import ‘data.table::first’ by ‘dplyr::first’ when loading ‘PloidyPeaks’
Warning: replacing previous import ‘data.table::last’ by ‘dplyr::last’ when loading ‘PloidyPeaks’
Warning: replacing previous import ‘data.table::between’ by ‘dplyr::between’ 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...
* 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; 2721 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...
* 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 10 NOTES
i See the PloidyPeaks.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.