===============================
R CMD BUILD
===============================
* checking for file ‘plaid/DESCRIPTION’ ... OK
* preparing ‘plaid’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
* creating vignettes ... OK
* excluding invalid files
Subdirectory 'inst/doc' contains invalid file names:
‘01_plaid-vignette.Rmd’ ‘02_compare-vignette.Rmd’
‘01_plaid-vignette.html’ ‘02_compare-vignette.html’
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘plaid_0.99.5.tar.gz’
===============================
BiocCheckGitClone('plaid')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid
→ BiocVersion: 3.22
→ Package: plaid
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid
→ 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 v1.47.1 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/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid.Rcheck’
* using R version 4.5.1 Patched (2025-08-23 r88802)
* 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 ‘plaid/DESCRIPTION’ ... OK
* this is package ‘plaid’ version ‘0.99.5’
* 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 ‘plaid’ can be installed ... WARNING
Found the following significant warnings:
Warning: replacing previous import ‘matrixStats::colRanks’ by ‘sparseMatrixStats::colRanks’ when loading ‘plaid’
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid.Rcheck/00install.out’ for details.
* checking installed package size ... INFO
installed size is 6.0Mb
sub-directories of 1Mb or more:
logo 5.3Mb
* checking package directory ... OK
* checking for future file timestamps ... NOTE
unable to verify current time
* 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 ... WARNING
Subdirectory 'inst/doc' contains invalid file names:
‘01_plaid-vignette.Rmd’ ‘02_compare-vignette.Rmd’
‘01_plaid-vignette.html’ ‘02_compare-vignette.html’
Please remove or rename the files.
See section ‘Package subdirectories’ in the ‘Writing R Extensions’
manual.
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [7s/7s] OK
* checking whether the package can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [7s/7s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [7s/7s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Namespace in Imports field not imported from: ‘SingleCellExperiment’
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 ... [26s/26s] NOTE
dual_test: no visible global function definition for ‘is’
dual_test: no visible binding for global variable ‘wt0’
gset_averageCLR: no visible global function definition for
‘colSignedRanks’
Undefined global functions or variables:
colSignedRanks is wt0
Consider adding
importFrom("methods", "is")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [18s/18s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [18s/15s]
[18s/15s] 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, 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid.Rcheck/00check.log’
for details.
===============================
BiocCheck('plaid_0.99.5.tar.gz')
===============================
── Installing plaid ────────────────────────────────────────────────────────────
✔ Package installed successfully
── plaid session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpgRDBi2/file198c844137123a/plaid
→ BiocVersion: 3.22
→ Package: plaid
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/97aa187cf7add748683f3205cbe3fbeecb1be097/plaid.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpgRDBi2/file198c844137123a/plaid
→ installDir: /tmp/RtmpgRDBi2/file198c841f75dae
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on plaid ──────────────────────────────────────────────────
* 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...
i NOTE: Update R version dependency from 4.1.0 to 4.5.0
* 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...
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (50%).
* 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:
• 01_plaid-vignette.Rmd
• 02_compare-vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of plaid...
* Checking coding practice...
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/stats.R (line 230, column 13)
• R/stats.R (line 233, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/plaid.R (line 125, column 13)
• ...
• R/stats.R (line 440, column 33)
* 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 5
functions greater than 50 lines.
The longest 5 functions are:
• dual_test() (R/stats.R): 80 lines
• ...
• .convert_geneset_to_matrix() (R/bioc-utils.R): 53 lines
* Checking man page documentation...
Warning: replacing previous import ‘matrixStats::colRanks’ by ‘sparseMatrixStats::colRanks’ when loading ‘plaid’
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• read.gmt.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 16% of man
pages use at least one of these tags.
Found in files:
• dualGSEA.Rd
• ...
• write.gmt.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; 121 lines (6%) are > 80 characters long.
First few lines:
• R/bioc-utils.R#L15 #' @param object A Bioconductor object ( ...
• ...
• vignettes/02_compare-vignette.Rmd#L87 Altogether, these data demonstrate the
m ...
i NOTE: Consider multiples of 4 spaces for line indents; 496 lines (23%) are
not.
First few lines:
• R/bioc-utils.R#L39 ...
• ...
• vignettes/02_compare-vignette.Rmd#L16 comment = "#>" ...
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...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.47.1 results ───────────────────────────────────────────────────
✖ 2 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the plaid.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.