===============================
R CMD BUILD
===============================
* checking for file ‘barmixR/DESCRIPTION’ ... OK
* preparing ‘barmixR’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘barmixR_0.99.0.tar.gz’
===============================
BiocCheckGitClone('barmixR')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/barmixR_20260504171736/barmixR
→ BiocVersion: 3.23
→ Package: barmixR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/barmixR_20260504171736/barmixR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/barmixR_20260504171736/barmixR
→ 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 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 v1.49.4 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/barmixR_20260504171736/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: 2026-05-04 17:23:08 UTC
* using option ‘--no-vignettes’
* checking for file ‘barmixR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘barmixR’ 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 ‘barmixR’ 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 ... NOTE
File
LICENSE
is not mentioned in the DESCRIPTION file.
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking code files for non-ASCII characters ... WARNING
Found the following files with non-ASCII characters:
R/QTRresistance.R
R/fractionRatio.R
R/populationRatio.R
R/ppcPopulation.R
Portable packages must use only ASCII characters in their R code and
NAMESPACE directives, except perhaps in comments.
Use \uxxxx escapes for other characters.
Function ‘tools::showNonASCIIfile’ can help in finding non-ASCII
characters in files.
* 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 ... [6s/6s] NOTE
QTRDecision: no visible binding for global variable ‘cell’
QTRDecision: no visible binding for global variable ‘median’
QTRDecision : <anonymous>: no visible binding for global variable
‘lower_whisker’
QTRDecision : <anonymous>: no visible binding for global variable ‘q25’
QTRDecision : <anonymous>: no visible binding for global variable ‘y’
QTRDecision : <anonymous>: no visible binding for global variable ‘q75’
QTRDecision : <anonymous>: no visible binding for global variable
‘upper_whisker’
QTRDecision : <anonymous>: no visible binding for global variable
‘median’
QTRheatmap: no visible binding for global variable ‘treat’
QTRheatmap: no visible binding for global variable ‘new’
QTRheatmap: no visible binding for global variable ‘new1’
QTRheatmap: no visible binding for global variable ‘Mean’
QTRheatmap: no visible binding for global variable ‘Direction’
QTRresistance: no visible binding for global variable ‘treat’
QTRresistance: no visible binding for global variable ‘keep’
QTRresistance: no visible global function definition for ‘median’
QTRresistance: no visible global function definition for ‘sd’
barmixRQTR: no visible global function definition for ‘modifyList’
fractionRatio: no visible binding for global variable ‘treat’
fractionRatio: no visible binding for global variable ‘p_ratio’
fractionRatio: no visible binding for global variable ‘keep’
populationRatio: no visible binding for global variable ‘treat’
populationRatio: no visible binding for global variable ‘p_ratio’
populationRatio: no visible binding for global variable ‘CDF’
populationRatio: no visible binding for global variable ‘keep’
ppcBarcodes: no visible global function definition for ‘ave’
ppcBarcodes: no visible binding for global variable ‘cell’
ppcBarcodes: no visible binding for global variable ‘pred’
ppcBarcodes: no visible binding for global variable ‘count’
ppcPopulation: no visible binding for global variable ‘treatment’
ppcPopulation: no visible binding for global variable
‘predicted_population’
ppcPopulation: no visible binding for global variable ‘treat’
Undefined global functions or variables:
CDF Direction Mean ave cell count keep lower_whisker median
modifyList new new1 p_ratio pred predicted_population q25 q75 sd
treat treatment upper_whisker y
Consider adding
importFrom("methods", "new")
importFrom("stats", "ave", "median", "sd")
importFrom("utils", "modifyList")
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 ... WARNING
Missing link(s) in Rd file 'QTRDecision.Rd':
‘barmixR_fit’
Missing link(s) in Rd file 'QTRheatmap.Rd':
‘barmixR_fit’
Missing link(s) in Rd file 'QTRresistance.Rd':
‘barmixR_fit’
Missing link(s) in Rd file 'fractionRatio.Rd':
‘barmixR_fit’
Missing link(s) in Rd file 'populationRatio.Rd':
‘barmixR_fit’
Missing link(s) in Rd file 'ppcPopulation.Rd':
‘barmixR_fit’
See section 'Cross-references' in the 'Writing R Extensions' manual.
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'QTRDecision.Rd'
‘model’
Documented arguments not in \usage in Rd file 'QTRDecision.Rd':
‘@param’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... ERROR
TIMEOUT: R CMD check exceeded 15 mins
===============================
BiocCheck('barmixR_0.99.0.tar.gz')
===============================
── Installing barmixR ──────────────────────────────────────────────────────────
✔ Package installed successfully
── barmixR session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpODMqqR/file254c55444e715/barmixR
→ BiocVersion: 3.23
→ Package: barmixR
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/4215/barmixR_20260504171736/barmixR.BiocCheck
→ BiocCheckVersion: 1.49.4
→ sourceDir: /tmp/RtmpODMqqR/file254c55444e715/barmixR
→ installDir: /tmp/RtmpODMqqR/file254c5511484d8a
→ 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...
i NOTE: Consider adding these automatically suggested biocViews:
CellBasedAssays, Normalization, Preprocessing
i Search 'biocViews' at https://contributions.bioconductor.org
* 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 (14%).
* 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...
* 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): 326 lines
• ...
• QTRDecision() (R/QTRDecision.R): 178 lines
* Checking man page documentation...
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* 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; 115 lines (4%) are > 80 characters long.
First few lines:
• R/barmixRQTR.R#L187 #' ## Note: iteration numbers are intent ...
• ...
• vignettes/barmixR-workflow.Rmd#L408 In translational and pharmaceutical
sett ...
i NOTE: Consider multiples of 4 spaces for line indents; 962 lines (30%) are
not.
First few lines:
• R/barmixRQTR.R#L221 ## ---------- helpers ---------- ...
• ...
• vignettes/barmixR-workflow.Rmd#L394 # 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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
i Maintainer is registered at support site.
i Package is in the Support Site Watched Tags.
── BiocCheck v1.49.4 results ───────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 0 WARNINGS | i 9 NOTES
i See the barmixR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.