===============================
BiocCheckGitClone('PloidyPeaks')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks
→ BiocVersion: 3.20
→ Package: PloidyPeaks
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks/.gitignore'
✖ ERROR: System files found that should not be Git tracked.
• PloidyPeaks.Rproj
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘PloidyPeaks/DESCRIPTION’ ... OK
* this is package ‘PloidyPeaks’ 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 ... 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 ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/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 ... [3s/3s] 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 ... [3s/3s] OK
* checking loading without being on the library search path ... [3s/3s] 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 ... [19s/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:
url <- "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/analysis/ploidyPeaksOutput.csv"
Rd file 'massFlowGraph.Rd':
\examples lines wider than 100 characters:
url <- "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/analysis/ploidyPeaksOutput.csv"
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 ... [14s/17s] ERROR
Running examples in ‘PloidyPeaks-Ex.R’ failed
The error most likely occurred in:
> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: rectGateFlowSet
> ### Title: rectGateFlowSet
> ### Aliases: rectGateFlowSet
>
> ### ** Examples
>
> library(BiocFileCache)
Loading required package: dbplyr
> bfc <- BiocFileCache()
> urls <- c(
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_1.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_2.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_3.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_4.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_5.fcs",
+ "https://ploidypeaksvignette.blob.core.windows.net/ploidypeaksvignettedata/raw_data/A1_6.fcs"
+ )
> folderPath <- file.path(bfc@cache, "raw_data")
> dir.create(folderPath, showWarnings = FALSE, recursive = TRUE)
> cachedFiles <- sapply(urls, function(url) {
+ cachedFile <- bfcadd(bfc, url)
+ targetFile <- file.path(folderPath, basename(url))
+ if (!file.exists(targetFile)) file.copy(cachedFile, targetFile)
+ })
> rectGateFlowSet(
+ rawDir = folderPath,
+ xVariable = "FITC-A",
+ yVariable = "SSC-A",
+ xMinValue = 50,
+ xMaxValue = 800,
+ yMinValue = 50,
+ yMaxValue = 800,
+ savePlot = FALSE
+ )
Error in readFCSheader(con) :
This does not seem to be a valid FCS2.0, FCS3.0 or FCS3.1 file
Calls: rectGateFlowSet ... <Anonymous> -> suppressMessages -> withCallingHandlers
Execution halted
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [2s/2s]
[2s/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 ... [2s/3s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 4 NOTEs
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks.Rcheck/00check.log’
for details.
===============================
BiocCheck('PloidyPeaks_0.99.0.tar.gz')
===============================
── Installing PloidyPeaks ──────────────────────────────────────────────────────
✔ Package installed successfully
── PloidyPeaks session metadata ────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpiEALN7/file4aa526258d5bf/PloidyPeaks
→ BiocVersion: 3.20
→ Package: PloidyPeaks
→ PackageVersion: 0.99.0
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3567/PloidyPeaks_20240930082120/PloidyPeaks.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpiEALN7/file4aa526258d5bf/PloidyPeaks
→ installDir: /tmp/RtmpiEALN7/file4aa52d32d17b
→ 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...
! WARNING: Package files exceed the 5MB size limit.
Files over the limit:
• /tmp/RtmpiEALN7/file4aa526258d5bf/PloidyPeaks//inst/doc/ploidyPeaks.html
• /tmp/RtmpiEALN7/file4aa526258d5bf/PloidyPeaks/inst/doc/ploidyPeaks.html
• /tmp/RtmpiEALN7/file4aa526258d5bf/PloidyPeaks/inst/doc/ploidyPeaks.html
* 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: OneChannel,
MultipleComparison
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...
i NOTE: Provide 'URL', 'BugReports' 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Evaluate more vignette chunks.
i 19 out of 33 code chunks = 57% unevaluated
i 0 non-exec code chunk(s) (e.g., '```r')
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/ploidyPeaks.Rmd (code line 223, column 73)
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/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 108, column 24)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• flowLineGraph.R (line 726, column 15)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/flowLineGraph.R (line 737, column 7)
• ...
• print() in R/RSEOutlierDetection.R (line 134, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/flowLineGraph.R (line 82, column 15)
• ...
• R/RSEOutlierDetection.R (line 64, column 21)
* Checking parsed R code in R directory, examples, vignettes...
i Found @ in man/flowLineGraph.Rd
i Found @ in man/flowPeakDetection.Rd
i Found @ in man/peakCorrection.Rd
i Found @ in man/rectGateFlowFrame.Rd
i Found @ in man/rectGateFlowSet.Rd
i NOTE: Use accessors; don't access S4 class slots via '@' in
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): 1335 lines
• ...
• .popConfidence3Pop() (R/flowPeakDetection.R): 527 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’
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• massFlowGraph.Rd
• RSEOutlierDetection.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 29% of man
pages use at least one of these tags.
Found in files:
• massFlowGraph.Rd
• RSEOutlierDetection.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• massFlowGraph.Rd
• RSEOutlierDetection.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; 184 lines (2%) are > 80 characters long.
First few lines:
• R/flowLineGraph.R#L47 #' "https://ploidypeaksvignette.blob.c ...
• ...
• vignettes/ploidyPeaks.Rmd#L503 Now, we can look at the *.csv* files, pl ...
i NOTE: Consider multiples of 4 spaces for line indents; 2899 lines (26%) are
not.
First few lines:
• R/flowLineGraph.R#L98 getwd() ...
• ...
• vignettes/ploidyPeaks.Rmd#L487 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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.41.17 results ──────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 3 WARNINGS | • 14 NOTES
i See the PloidyPeaks.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.