===============================
R CMD BUILD
===============================
* checking for file ‘CellMentor/DESCRIPTION’ ... OK
* preparing ‘CellMentor’:
* 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 ‘CellMentor_0.99.0.tar.gz’
===============================
BiocCheckGitClone('CellMentor')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3995/CellMentor_20251121165620/CellMentor
→ BiocVersion: 3.23
→ Package: CellMentor
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3995/CellMentor_20251121165620/CellMentor.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3995/CellMentor_20251121165620/CellMentor
→ 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 v1.47.1 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/3995/CellMentor_20251121165620/CellMentor.Rcheck’
* using R Under development (unstable) (2025-10-20 r88955)
* 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 ‘CellMentor/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CellMentor’ 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 ‘CellMentor’ 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 ... [22s/23s] OK
* checking whether the package can be loaded with stated dependencies ... [20s/20s] OK
* checking whether the package can be unloaded cleanly ... [20s/20s] OK
* checking whether the namespace can be loaded with stated dependencies ... [20s/20s] OK
* checking whether the namespace can be unloaded cleanly ... [22s/22s] OK
* checking loading without being on the library search path ... [22s/22s] 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 ... [71s/72s] 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... [21s/22s] OK
* checking data for ASCII and uncompressed saves ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [62s/64s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
CellMentor 10.423 0.070 11.002
h.baron_dataset 7.490 1.785 9.597
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [223s/231s]
[223s/231s] 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: OK
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('CellMentor_0.99.0.tar.gz')
===============================
── Installing CellMentor ───────────────────────────────────────────────────────
✔ Package installed successfully
── CellMentor session metadata ─────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpujnyoD/file2ffbcc17e9fa26/CellMentor
→ BiocVersion: 3.23
→ Package: CellMentor
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3995/CellMentor_20251121165620/CellMentor.BiocCheck
→ BiocCheckVersion: 1.47.1
→ sourceDir: /tmp/RtmpujnyoD/file2ffbcc17e9fa26/CellMentor
→ installDir: /tmp/RtmpujnyoD/file2ffbcc1fa42659
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on CellMentor ─────────────────────────────────────────────
* 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: Sequencing,
DNASeq, CellBiology, Clustering
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 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 (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:
• CellMentor_vignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of CellMentor...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/GridSearch.R (line 202, 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 12
functions greater than 50 lines.
The longest 5 functions are:
• CellMentor() (R/GridSearch.R): 167 lines
• ...
• initialize_nndsvd() (R/InitializeWH.R): 105 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• cm_rank.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 14% of man
pages use at least one of these tags.
Found in files:
• cm_rank.Rd
• obj_toy.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• cm_rank.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; 37 lines (1%) are > 80 characters long.
First few lines:
• R/CellMentor-package.R#L12 #' \item \strong{Supervised NMF Framew ...
• ...
• vignettes/CellMentor_vignette.Rmd#L302 doi:
[https://doi.org/10.1101/2025.06.17 ...
i NOTE: Consider multiples of 4 spaces for line indents; 1288 lines (32%) are
not.
First few lines:
• R/classes.R#L36 slots = c( ...
• ...
• vignettes/CellMentor_vignette.Rmd#L284 X = data_matrix(matrices(best_model))
...
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 v1.47.1 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 11 NOTES
i See the CellMentor.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.