===============================
R CMD BUILD
===============================
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* preparing ‘scDiagnostics’:
* 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
* building ‘scDiagnostics_0.99.8.tar.gz’
===============================
BiocCheckGitClone('scDiagnostics')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/373d086b2c99eeaed5634261743fe466f0a72685/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/373d086b2c99eeaed5634261743fe466f0a72685/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/373d086b2c99eeaed5634261743fe466f0a72685/scDiagnostics
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3449/373d086b2c99eeaed5634261743fe466f0a72685/scDiagnostics.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.4 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘scDiagnostics/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘scDiagnostics’ version ‘0.99.8’
* 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 whether package ‘scDiagnostics’ 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 ... 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 ... [6s/6s] OK
* checking whether the package can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the package can be unloaded cleanly ... [6s/6s] OK
* checking whether the namespace can be loaded with stated dependencies ... [6s/6s] OK
* checking whether the namespace can be unloaded cleanly ... [6s/6s] OK
* checking loading without being on the library search path ... [6s/6s] 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 ... [24s/24s] OK
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [6s/6s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [91s/83s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
plotCellTypeMDS 11.711 0.140 11.851
calculateCellDistances 9.441 0.379 9.505
calculateCramerPValue 4.907 0.112 5.020
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [98s/85s]
[98s/85s] 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: OK
===============================
BiocCheck('scDiagnostics_0.99.8.tar.gz')
===============================
── Installing scDiagnostics ────────────────────────────────────────────────────
✔ Package installed successfully
── scDiagnostics session metadata ──────────────────────────────────────────────
→ sourceDir: /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics
→ BiocVersion: 3.20
→ Package: scDiagnostics
→ PackageVersion: 0.99.8
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3449/373d086b2c99eeaed5634261743fe466f0a72685/scDiagnostics.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics
→ installDir: /tmp/RtmptBHDUN/file2f92f846fa947c
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on scDiagnostics ──────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
PrincipalComponent, Regression
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...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (20%).
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/AnnotationAnomalies.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/CellDistancesDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/DatasetMarkerGeneAlignment.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/QCandAnnotationScores.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/scDiagnostics.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/StatisticalMeasures.Rmd
Warning in checkVigEvalAllFalse(.BiocPackage) :
More than one `opts_chunk$set()` in /tmp/RtmptBHDUN/file2f92f8353b73bb/scDiagnostics/vignettes/VisualizationTools.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of scDiagnostics...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• boxplotPCA.R (line 50, column 36)
• ...
• regressPC.R (line 89, column 35)
* 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 32
functions greater than 50 lines.
The longest 5 functions are:
• argumentCheck() (R/argumentCheck.R): 175 lines
• ...
• plotWassersteinDistance() (R/plotWassersteinDistance.R): 140 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; 1159 lines (15%) are > 80 characters long.
First few lines:
• R/argumentCheck.R#L4 #' This function validates the input arg ...
• ...
• vignettes/VisualizationTools.Rmd#L277 ```{r SessionInfo, echo=FALSE,
message=F ...
i NOTE: Consider multiples of 4 spaces for line indents; 778 lines (10%) are
not.
First few lines:
• R/argumentCheck.R#L48 reference_data ...
• ...
• vignettes/VisualizationTools.Rmd#L245 cell_type = "B_and_plasma" ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 6 NOTES
i See the scDiagnostics.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.