===============================
R CMD BUILD
===============================
* checking for file ‘barmixR/DESCRIPTION’ ... OK
* preparing ‘barmixR’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package (it is needed to build vignettes)
* creating vignettes ... OK
* cleaning src
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
Omitted ‘LazyData’ from DESCRIPTION
* building ‘barmixR_0.99.1.tar.gz’
===============================
BiocCheckGitClone('barmixR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR
→ BiocVersion: 3.23
→ Package: barmixR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR/.gitignore'
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* Checking for remote package usage...
* 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 v1.49.6 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/4215/263669ca2e12b031d900505004161000042b1356/barmixR.Rcheck’
* using R version 4.6.0 RC (2026-04-17 r89917)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
GNU Fortran (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0
* running under: Ubuntu 24.04.4 LTS
* using session charset: UTF-8
* current time: 2026-05-18 18:06:49 UTC
* using option ‘--no-vignettes’
* checking for file ‘barmixR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barmixR’ version ‘0.99.1’
* 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 ‘barmixR’ can be installed ... OK
* used C++ compiler: ‘g++ (Ubuntu 13.3.0-6ubuntu2~24.04.1) 13.3.0’
* checking C++ specification ... INFO
specified C++17
* checking installed package size ... INFO
installed size is 48.4Mb
sub-directories of 1Mb or more:
help 1.4Mb
libs 46.6Mb
* 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 ... [3s/3s] OK
* checking whether the package can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the package can be unloaded cleanly ... [3s/3s] OK
* checking whether the namespace can be loaded with stated dependencies ... [3s/3s] OK
* checking whether the namespace can be unloaded cleanly ... [3s/3s] OK
* checking loading without being on the library search path ... [4s/4s] OK
* checking whether startup messages can be suppressed ... [3s/3s] 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 ... [13s/11s] 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 line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... INFO
GNU make is a SystemRequirements.
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking use of PKG_*FLAGS in Makefiles ... OK
* checking use of SHLIB_OPENMP_*FLAGS in Makefiles ... OK
* checking pragmas in C/C++ headers and code ... OK
* checking compilation flags used ... NOTE
Compilation used the following non-portable flag(s):
‘-Werror=format-security’
* checking compiled code ... INFO
Note: information on .o files is not available
* checking files in ‘vignettes’ ... OK
* checking examples ... [50s/50s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
QTRDecision 6.974 0.093 7.067
QTRheatmap 5.799 0.041 5.841
QTRresistance 5.393 0.058 5.451
ppcBarcodes 5.282 0.022 5.304
fractionRatio 5.228 0.040 5.268
populationRatio 5.035 0.020 5.056
ppcPopulation 5.028 0.006 5.038
* 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR.Rcheck/00check.log’
for details.
===============================
BiocCheck('barmixR_0.99.1.tar.gz')
===============================
── Installing barmixR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── barmixR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpbmViZk/file2b2f9f42bc6a66/barmixR
→ BiocVersion: 3.23
→ Package: barmixR
→ PackageVersion: 0.99.1
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/263669ca2e12b031d900505004161000042b1356/barmixR.BiocCheck
→ BiocCheckVersion: 1.49.6
→ sourceDir: /tmp/RtmpbmViZk/file2b2f9f42bc6a66/barmixR
→ installDir: /tmp/RtmpbmViZk/file2b2f9f92cb811
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on barmixR ────────────────────────────────────────────────
* 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 4.3.0 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 if 'Package:' field matches directory / tarball...
* 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 (8%).
* 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:
• barmixR-workflow.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of barmixR...
* Checking coding practice...
i NOTE: Avoid sapply(); use vapply()
Found in files:
• R/stanmodels.R (line 12, column 15)
* 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 9
functions greater than 50 lines.
The longest 5 functions are:
• barmixRQTR() (R/barmixRQTR.R): 313 lines
• ...
• QTRDecision() (R/QTRDecision.R): 178 lines
* Checking man page documentation...
* Checking package NEWS...
* Checking unit tests...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 139 lines (3%) are > 80 characters long.
First few lines:
• R/barmixRQTR.R#L187 #' ## Note: iteration numbers are intent ...
• ...
• vignettes/barmixR-workflow.Rmd#L409 In translational and pharmaceutical
sett ...
i NOTE: Consider multiples of 4 spaces for line indents; 1200 lines (26%) are
not.
First few lines:
• R/barmixRQTR.R#L223 ## ---------- helpers ---------- ...
• ...
• vignettes/barmixR-workflow.Rmd#L395 # legend_text = "DMSO = control
condit ...
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...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.49.6 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 8 NOTES
i See the barmixR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.