===============================
R CMD BUILD
===============================
* checking for file ‘DOtools/DESCRIPTION’ ... OK
* preparing ‘DOtools’:
* 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 ‘DOtools_0.99.10.tar.gz’
===============================
BiocCheckGitClone('DOtools')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools
→ BiocVersion: 3.22
→ Package: DOtools
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools
→ 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 v1.45.18 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/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools.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 ‘DOtools/DESCRIPTION’ ... OK
* this is package ‘DOtools’ version ‘0.99.10’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 35 non-default packages.
Importing from so many packages makes the package vulnerable to any of
them becoming unavailable. Move as many as possible to Suggests and
use conditionally.
* checking if this is a source package ... OK
* checking if there is a namespace ... OK
* checking for hidden files and directories ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘DOtools’ can be installed ... NOTE
Found the following notes/warnings:
Non-staged installation was used
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools.Rcheck/00install.out’ for details.
* 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 ... [12s/12s] OK
* checking whether the package can be loaded with stated dependencies ... [11s/11s] OK
* checking whether the package can be unloaded cleanly ... [11s/11s] OK
* checking whether the namespace can be loaded with stated dependencies ... [12s/12s] OK
* checking whether the namespace can be unloaded cleanly ... [12s/12s] OK
* checking loading without being on the library search path ... [12s/12s] OK
* checking whether startup messages can be suppressed ... [12s/12s] 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 ... [43s/43s] 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 line endings in shell scripts ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [113s/123s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
DO.Integration 22.972 0.862 23.836
DO.CellComposition 8.503 4.351 8.050
DO.SplitBarGSEA 6.612 0.156 10.413
DO.enrichR 6.408 0.250 10.216
DO.MultiDGE 6.152 0.138 6.291
DO.CellTypist 4.140 0.622 12.612
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [98s/97s]
[98s/98s] 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 ... [4s/4s] OK
* DONE
Status: 3 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools.Rcheck/00check.log’
for details.
===============================
BiocCheck('DOtools_0.99.10.tar.gz')
===============================
── Installing DOtools ──────────────────────────────────────────────────────────
✔ Package installed successfully
── DOtools session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp8FfKzd/file12e1317761a4cf/DOtools
→ BiocVersion: 3.22
→ Package: DOtools
→ PackageVersion: 0.99.10
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3869/3dea7b8e77e52daa74aae8394ada9e73d76aba04/DOtools.BiocCheck
→ BiocCheckVersion: 1.45.18
→ sourceDir: /tmp/Rtmp8FfKzd/file12e1317761a4cf/DOtools
→ installDir: /tmp/Rtmp8FfKzd/file12e13142add0d7
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on DOtools ────────────────────────────────────────────────
* 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...
* 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 (18%).
* Checking for pinned package versions in DESCRIPTION...
* Checking for 'fnd' role in Authors@R...
* 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 DOtools...
* Checking coding practice...
* 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 25
functions greater than 50 lines.
The longest 5 functions are:
• DO.Dotplot() (R/DO.Dotplot.R): 915 lines
• ...
• DO.CellComposition() (R/DO.CellComposition.R): 487 lines
* Checking man page documentation...
Registered S3 method overwritten by 'zellkonverter':
method from
py_to_r.pandas.core.arrays.categorical.Categorical reticulate
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• DO.CellBender.Rd
• DO.Import.Rd
• DO.scVI.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 11% of man
pages use at least one of these tags.
Found in files:
• DO.CellBender.Rd
• DO.Import.Rd
• DO.scVI.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• DO.CellBender.Rd
• DO.Import.Rd
• DO.scVI.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...
* 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 v1.45.18 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 4 NOTES
i See the DOtools.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.