===============================
R CMD BUILD
===============================
* checking for file singIST/DESCRIPTION ... OK
* preparing singIST:
* 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
Omitted LazyData from DESCRIPTION
* building singIST_0.99.5.tar.gz
===============================
BiocCheckGitClone('singIST')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST
BiocVersion: 3.22
Package: singIST
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST
installDir: NULL
isTarBall: FALSE
platform: unix
* Checking valid files...
ERROR: System files found that should not be Git tracked.
man/.Rhistory
* 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
1 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/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST.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 singIST/DESCRIPTION ... OK
* this is package singIST version 0.99.5
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 21 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package singIST can be installed ... OK
* 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 ... [16s/16s] OK
* checking whether the package can be loaded with stated dependencies ... [14s/14s] OK
* checking whether the package can be unloaded cleanly ... [14s/14s] OK
* checking whether the namespace can be loaded with stated dependencies ... [15s/15s] OK
* checking whether the namespace can be unloaded cleanly ... [16s/16s] OK
* checking loading without being on the library search path ... [15s/15s] OK
* checking whether startup messages can be suppressed ... [15s/15s] 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 ... [50s/50s] 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 files in vignettes ... OK
* checking examples ... [130s/179s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
multiple_singISTrecapitulations 15.658 0.656 21.737
celltype_recap 8.168 0.666 13.313
derive_contributions 7.731 0.314 10.363
singIST_treat 7.819 0.215 12.030
superpathway_recap 7.839 0.188 10.254
gene_contrib 7.787 0.184 12.322
derive_scores 7.688 0.245 10.318
singISTrecapitulations 7.703 0.116 10.057
helpers 5.816 0.317 27.047
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running testthat.R [76s/93s]
[76s/94s] 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] WARNING
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
! LaTeX Error: Unicode character (U+03B3)
not set up for use with LaTeX.
See the LaTeX manual or LaTeX Companion for explanation.
Type H <return> for immediate help.
* checking PDF version of manual without index ... ERROR
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST.Rcheck/00check.log
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('singIST_0.99.5.tar.gz')
===============================
Installing singIST
Package installed successfully
singIST session metadata
sourceDir: /tmp/RtmpevM5QY/file10863457c1dc37/singIST
BiocVersion: 3.22
Package: singIST
PackageVersion: 0.99.5
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/d85edec87cd43493d83b70c9917dc01c1004b194/singIST.BiocCheck
BiocCheckVersion: 1.47.1
sourceDir: /tmp/RtmpevM5QY/file10863457c1dc37/singIST
installDir: /tmp/RtmpevM5QY/file10863425e966dd
isTarBall: TRUE
platform: unix
Running BiocCheck on singIST
* 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 4.2 to 4.5.0
* 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 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 (39%).
* 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:
singISTvignette.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of singIST...
* Checking coding practice...
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
R/helpers.R (line 1166, column 46)
* 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 7
functions greater than 50 lines.
The longest 5 functions are:
pseudobulk_log2FC() (R/helpers.R): 55 lines
...
fitOptimal.superpathway.input() (R/bbb-step1-fit.R): 52 lines
* Checking man page documentation...
ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
asmbPLSDA.cv.kcv.Rd
...
setRepeatGeneSets-method.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 10% of man
pages use at least one of these tags.
Found in files:
orthology_mapping.Rd
...
setRepeatGeneSets-method.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; 5 lines (0%) are > 80 characters long.
First few lines:
R/bbb-step1-fit.R#L265 #' \donttest{asmbPLSDA.cv.kcv(X.matrix, ...
...
R/helpers.R#L1583 predictor_block[samples, ...
i NOTE: Consider multiples of 4 spaces for line indents; 26 lines (1%) are not.
First few lines:
R/bbb-step1-fit.R#L27 cellt ...
...
vignettes/singISTvignette.Rmd#L215 ...
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
1 ERRORS | 0 WARNINGS | i 8 NOTES
i See the singIST.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.