===============================
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
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
NB: this package now depends on R (>= 3.5.0)
WARNING: Added dependency on R >= 3.5.0 because serialized objects in
serialize/load version 3 cannot be read in older versions of R.
File(s) containing such objects:
‘plaid/inst/extdata/pbmc3k-50cells.rda’
* building ‘plaid_0.99.0.tar.gz’
===============================
BiocCheckGitClone('plaid')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid
→ BiocVersion: 3.22
→ Package: plaid
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid/.gitignore'
* 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 v1.45.18 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/3943/plaid_20251003162229/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 ‘0.99.0’
* 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 whether package ‘plaid’ can be installed ... OK
* checking installed package size ... OK
* 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 ... OK
* checking code files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] 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 ... [3s/3s] NOTE
dual_test: no visible global function definition for ‘is’
dual_test: no visible binding for global variable ‘wt0’
fc_ttest: no visible global function definition for ‘p.adjust’
fc_ttest: no visible binding for global variable ‘matG’
gset_averageCLR: no visible global function definition for
‘colSignedRanks’
matrix_metap: no visible global function definition for ‘pchisq’
matrix_metap: no visible binding for global variable ‘qnorm’
matrix_metap: no visible global function definition for ‘pnorm’
matrix_onesample_ttest : <anonymous>: no visible global function
definition for ‘pt’
replaid.gsva : <anonymous>: no visible global function definition for
‘ecdf’
Undefined global functions or variables:
colSignedRanks ecdf is matG p.adjust pchisq pnorm pt qnorm wt0
Consider adding
importFrom("methods", "is")
importFrom("stats", "ecdf", "p.adjust", "pchisq", "pnorm", "pt",
"qnorm")
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 files in ‘vignettes’ ... OK
* checking examples ... [4s/3s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [0s/0s]
[1s/1s] 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: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid.Rcheck/00check.log’
for details.
===============================
BiocCheck('plaid_0.99.0.tar.gz')
===============================
── Installing plaid ────────────────────────────────────────────────────────────
✔ Package installed successfully
── plaid session metadata ──────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAApmLo/file3b760d63e396f0/plaid
→ BiocVersion: 3.22
→ Package: plaid
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3943/plaid_20251003162229/plaid.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/RtmpAApmLo/file3b760d63e396f0/plaid
→ installDir: /tmp/RtmpAApmLo/file3b760d4355d04c
→ 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 3.5.0 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...
* 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:
• compare-vignette.Rmd
• plaid-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 sapply(); use vapply()
Found in files:
• R/bioc-utils.R (line 157, column 17)
• ...
• R/gmt-utils.R (line 156, column 16)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• gmt-utils.R (line 47, column 56)
• ...
• stats.R (line 492, column 26)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/plaid.R (line 172, column 4)
• R/stats.R (line 222, column 13)
• R/stats.R (line 225, column 13)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/plaid.R (line 115, column 13)
• ...
• R/stats.R (line 422, 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: Empty or missing \value sections found in man page(s).
Found in files:
• man/write.gmt.Rd
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• dualGSEA.Rd
• read.gmt.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 20% of man
pages use at least one of these tags.
Found in files:
• dualGSEA.Rd
• ...
• write.gmt.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• dualGSEA.Rd
• ...
• write.gmt.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will 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; 121 lines (6%) are > 80 characters long.
First few lines:
• R/bioc-utils.R#L11 #' @param object A Bioconductor object ( ...
• ...
• vignettes/plaid-vignette.Rmd#L52 load(system.file("extdata", "pbmc3k-50ce ...
i NOTE: Consider multiples of 4 spaces for line indents; 497 lines (24%) are
not.
First few lines:
• R/bioc-utils.R#L35 ...
• ...
• vignettes/plaid-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...
i Unable to connect to the Bioc-devel mailing list: HTTP 502 Bad Gateway.
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 1 WARNINGS | i 14 NOTES
i See the plaid.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.