===============================
R CMD BUILD
===============================
* checking for file ‘singIST/DESCRIPTION’ ... OK
* preparing ‘singIST’:
* 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 ‘singIST_0.99.7.tar.gz’
===============================
BiocCheckGitClone('singIST')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST
→ BiocVersion: 3.23
→ Package: singIST
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST
→ 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 v1.47.7 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/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST.Rcheck’
* using R Under development (unstable) (2025-12-22 r89219)
* 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 ‘0.99.7’
* 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 ... 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 ... [15s/15s] 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 ... [14s/14s] OK
* checking whether the namespace can be unloaded cleanly ... [15s/15s] 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 ... NOTE
Namespaces in Imports field not imported from:
‘RcppAlgos’ ‘glmGamPoi’ ‘methods’ ‘sp’
All declared Imports should be used.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [51s/51s] 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 ... [69s/98s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
singIST_treat 8.233 0.459 14.176
helpers 6.242 0.484 30.272
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [17s/17s]
[17s/17s] 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: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST.Rcheck/00check.log’
for details.
===============================
BiocCheck('singIST_0.99.7.tar.gz')
===============================
── Installing singIST ──────────────────────────────────────────────────────────
✔ Package installed successfully
── singIST session metadata ────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpUQcWQk/file1af0a112ce2ca5/singIST
→ BiocVersion: 3.23
→ Package: singIST
→ PackageVersion: 0.99.7
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3826/c0f1484000663001ba02e1e60c3e54faf6a713ce/singIST.BiocCheck
→ BiocCheckVersion: 1.47.7
→ sourceDir: /tmp/RtmpUQcWQk/file1af0a112ce2ca5/singIST
→ installDir: /tmp/RtmpUQcWQk/file1af0a120c6888a
→ 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 4.5.0 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 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 6
functions greater than 50 lines.
The longest 5 functions are:
• biological_link_function() (R/step2-biologicalLink.R): 59 lines
• ...
• subsampling_CIP_GIP() (R/helpers.R): 53 lines
* Checking man page documentation...
i NOTE: Consider adding runnable examples to man pages that document exported
objects.
• multiple_fitOptimal.Rd
• ...
• restore_removed_columns.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 28% of man
pages use at least one of these tags.
Found in files:
• biological_link_function.Rd
• ...
• superpathway_recap.Rd
* Checking package NEWS...
* Checking unit tests...
* Checking skip_on_bioc() in tests...
i NOTE: skip_on_bioc() found in testthat files: test-asmbPLSDAcvloo.R
test-celltype_mapping.R test-celltype_recap.R test-CIP_GIP.R
test-derive_contributions.R test-derive_scores.R test-diff_expressed.R
test-gene_contrib.R test-hyperparameters.R test-mappingorganism.R
test-matrixToBlock.R test-multiple_check.R test-multiple_fitOptimal.R
test-multiple_singISTrecapitulations.R test-orthology_mapping.R test-pathway.R
test-permut_asmbplsda.R test-setGeneSetsCelltype.R test-singIST_treat.R
test-singISTrecapitulations.R test-superpathway_recap.R
test-superpathwayfitmodel.R test-superpathwayinput.R test-wilcox_CIP_GIP.R
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 56 lines (1%) are > 80 characters long.
First few lines:
• R/aaa-all-input.R#L6 #' @param dbsource Character. Database s ...
• ...
• vignettes/singISTvignette.Rmd#L535 $$t_i = \arg \min_{u_i \in \mathbb{R}^{n
...
i NOTE: Consider multiples of 4 spaces for line indents; 81 lines (2%) are not.
First few lines:
• R/aaa-all-input.R#L22 ...
• ...
• vignettes/singISTvignette.Rmd#L426 cytokine_superpath ...
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 v1.47.7 results ───────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | i 10 NOTES
i See the singIST.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.