===============================
R CMD BUILD
===============================
* checking for file daVis/DESCRIPTION ... OK
* preparing daVis:
* 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
* building daVis_0.99.0.tar.gz
===============================
BiocCheckGitClone('daVis')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4103/daVis_20260217184057/daVis
BiocVersion: 3.23
Package: daVis
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4103/daVis_20260217184057/daVis.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4103/daVis_20260217184057/daVis
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 v1.47.18 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/4103/daVis_20260217184057/daVis.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 daVis/DESCRIPTION ... OK
* checking extension type ... Package
* this is package daVis 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 daVis 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 ... [1s/1s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the namespace can be unloaded cleanly ... [1s/1s] OK
* checking loading without being on the library search path ... [1s/1s] 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 ... [9s/9s] OK
* checking Rd files ... [1s/1s] NOTE
checkRd: (-1) daLogRatioPlot.Rd:105: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:106: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:121-126: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:124: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:125: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:127-132: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:130: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daLogRatioPlot.Rd:131: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daVis-common-doc.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daVis-common-doc.Rd:18: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daVis-common-doc.Rd:19-24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) daVis-common-doc.Rd:22-23: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSEModel.Rd:24: Lost braces in \itemize; meant \describe ?
checkRd: (-1) getSEModel.Rd:25: Lost braces in \itemize; meant \describe ?
checkRd: (-1) labelTextLRP.Rd:16: Lost braces in \itemize; meant \describe ?
checkRd: (-1) labelTextLRP.Rd:17: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainLRP.Rd:20: Lost braces in \itemize; meant \describe ?
checkRd: (-1) mainLRP.Rd:21: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:28-33: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:31: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:32: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:34-39: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:37: Lost braces in \itemize; meant \describe ?
checkRd: (-1) orderFeatures.Rd:38: Lost braces in \itemize; meant \describe ?
checkRd: (-1) processFeatures.Rd:26-27: Lost braces in \itemize; meant \describe ?
checkRd: (-1) processFeatures.Rd:28: Lost braces in \itemize; meant \describe ?
checkRd: (-1) processFeatures.Rd:29-30: Lost braces in \itemize; meant \describe ?
* 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 ... [107s/110s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
daLogRatioPlot 13.856 0.137 14.246
daScatterPlot 13.698 0.056 13.973
daVolcanoPlot 12.384 0.051 12.964
daHeatmapLogFC 10.792 0.228 11.274
createExampleData 10.125 0.767 11.233
daMAplot 8.802 0.025 9.065
daSignificantGenesBarplot 8.745 0.020 9.001
daWaterfallPlot 8.367 0.016 8.613
daUpset 7.538 0.020 7.806
getSEModel 6.451 0.181 6.914
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [27s/28s]
[27s/28s] 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 ... [5s/5s] OK
* DONE
Status: 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/4103/daVis_20260217184057/daVis.Rcheck/00check.log
for details.
===============================
BiocCheck('daVis_0.99.0.tar.gz')
===============================
Installing daVis
Package installed successfully
daVis session metadata
sourceDir: /tmp/RtmpDo08QB/file28a97a6182b959/daVis
BiocVersion: 3.23
Package: daVis
PackageVersion: 0.99.0
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4103/daVis_20260217184057/daVis.BiocCheck
BiocCheckVersion: 1.47.18
sourceDir: /tmp/RtmpDo08QB/file28a97a6182b959/daVis
installDir: /tmp/RtmpDo08QB/file28a97a2b136799
isTarBall: TRUE
platform: unix
Running BiocCheck on daVis
* 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...
* 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...
Warning in readLines(con) :
URL 'http://bioconductor.org/js/versions.js': Timeout of 60 seconds was reached
* 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 (25%).
* 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 daVis...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/utils-topTables_extract.R (line 158, column 12)
...
R/utils-topTables_extract.R (line 278, column 15)
* Checking parsed R code in R directory, examples, vignettes...
i NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 2 times)
suppressMessages() in R/utils-exampleData.R (line 127, column 5)
suppressMessages() in R/utils-exampleData.R (line 242, column 10)
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There are 9
functions greater than 50 lines.
The longest 5 functions are:
daVolcanoPlot() (R/plots-volcanoPlot.R): 126 lines
...
createDataScatterPlot() (R/plots-scatterPlot.R): 92 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 4 spaces instead of tabs; 47 lines (1%) contain tabs.
First few lines:
R/plots-MAplot.R#L232 which(tbl[, featuresIdVar] %in% genesT ...
...
vignettes/daVis-vignette.Rmd#L668 featuresIdVar = "ENTREZID", n = 20) ...
i NOTE: Consider multiples of 4 spaces for line indents; 2200 lines (40%) are
not.
First few lines:
R/plots-genesBarplot.R#L45 input, ...
...
vignettes/daVis-vignette.Rmd#L764 addPercentage = TRUE ...
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...
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/bioc/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository https://bioconductor.org/packages/3.23/bioc
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/annotation/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/annotation
Warning in read.dcf(conn) :
URL 'http://bioconductor.org/packages/devel/data/experiment/VIEWS': Timeout of 60 seconds was reached
i Unable to access repository
https://bioconductor.org/packages/3.23/data/experiment
* Checking for bioc-devel mailing list subscription...
i Unable to connect to the Bioc-devel mailing list: Failed to perform HTTP
request. Caused by error in `curl::curl_fetch_memory()`: ! Timeout was reached
[stat.ethz.ch]: SSL connection timeout
* Checking for support site registration...
i Maintainer is registered at support site.
ERROR: Add package to Watched Tags in your Support Site profile; visit
https://support.bioconductor.org/accounts/edit/profile
BiocCheck v1.47.18 results
1 ERRORS | 0 WARNINGS | i 7 NOTES
i See the daVis.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.