===============================
R CMD BUILD
===============================
* checking for file DaparToolshed/DESCRIPTION ... OK
* preparing DaparToolshed:
* checking DESCRIPTION meta-information ... OK
* installing the package (it is needed 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
* looking to see if a data/datalist file should be added
* building DaparToolshed_0.99.28.tar.gz
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BiocCheckGitClone('DaparToolshed')
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sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3955/DaparToolshed_20260302173749/DaparToolshed
BiocVersion: 3.23
Package: DaparToolshed
PackageVersion: 0.99.28
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3955/DaparToolshed_20260302173749/DaparToolshed.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3955/DaparToolshed_20260302173749/DaparToolshed
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
DaparToolshed.Rproj
* 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...
* Checking that provided CITATION file is correctly formatted...
! WARNING: The 'doi' argument is missing or empty in the CITATION's
'bibentry()'. Only include a CITATION file if there is a preprint or
publication associated with this Bioconductor package.
BiocCheck v1.47.18 results
1 ERRORS | 1 WARNINGS | i 0 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory /home/pkgbuild/packagebuilder/workers/jobs/3955/DaparToolshed_20260302173749/DaparToolshed.Rcheck
* using R Under development (unstable) (2026-01-15 r89304)
* 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 DaparToolshed/DESCRIPTION ... OK
* checking extension type ... Package
* this is package DaparToolshed version 0.99.28
* 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 DaparToolshed 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 ... [8s/8s] OK
* checking whether the package can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the package can be unloaded cleanly ... [8s/8s] OK
* checking whether the namespace can be loaded with stated dependencies ... [8s/8s] OK
* checking whether the namespace can be unloaded cleanly ... [8s/8s] OK
* checking loading without being on the library search path ... [8s/8s] OK
* checking whether startup messages can be suppressed ... [8s/8s] 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 ... [35s/35s] OK
* checking Rd files ... [1s/1s] 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 ... [8s/8s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in vignettes ... OK
* checking examples ... [119s/117s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DaparToolshed-aggregate 23.885 0.306 24.193
wrapper.pirat 13.092 1.952 13.191
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [8s/8s]
[8s/8s] 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 ... [6s/6s] OK
* DONE
Status: OK
===============================
BiocCheck('DaparToolshed_0.99.28.tar.gz')
===============================
Installing DaparToolshed
Package installed successfully
DaparToolshed session metadata
sourceDir: /tmp/Rtmpy7a86v/fileb2217aceabc0/DaparToolshed
BiocVersion: 3.23
Package: DaparToolshed
PackageVersion: 0.99.28
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3955/DaparToolshed_20260302173749/DaparToolshed.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/Rtmpy7a86v/fileb2217aceabc0/DaparToolshed
installDir: /tmp/Rtmpy7a86v/fileb22144e578fd
isTarBall: TRUE
platform: unix
Running BiocCheck on DaparToolshed
* 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 4.5.0 to 4.6.0
* 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 (40%).
* 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...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of DaparToolshed...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
R/anova_analysis.R (line 77, column 36)
...
R/pepa.R (line 571, column 19)
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
aggregation.R (line 146, column 28)
aggregation.R (line 1428, column 56)
i NOTE: Avoid the use of 'paste' in condition signals
Found in files:
R/DaparToolshed_filter_qMetadata.R (line 116, column 18)
...
R/utils.R (line 452, column 12)
* 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 42
functions greater than 50 lines.
The longest 5 functions are:
hc_logFC_DensityPlot() (R/hypothesisTest_plot.R): 197 lines
...
pepa.test() (R/pepa.R): 149 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
man/SetHistory.Rd
Registered S3 method overwritten by 'quantmod':
method from
as.zoo.data.frame zoo
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
Add_Item_to_Dataset.Rd
...
wrapperClassic1wayAnova.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 7% of man
pages use at least one of these tags.
Found in files:
classic1wayAnova.Rd
...
wrapperClassic1wayAnova.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; 375 lines (3%) are > 80 characters long.
First few lines:
R/aggregation.R#L16 #' @param i The index or name of the ass ...
...
vignettes/DaparToolshed.Rmd#L478 SummarizedExperiment::rowData(obj[[lengt ...
i NOTE: Consider multiples of 4 spaces for line indents; 3984 lines (29%) are
not.
First few lines:
R/adjacencyMatrix.R#L22 X <- as.matrix(X) ...
...
vignettes/DaparToolshed.Rmd#L470 #create new assay with all values of in ...
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...
ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
BiocCheck v1.47.18 results
1 ERRORS | 1 WARNINGS | i 11 NOTES
i See the DaparToolshed.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.