===============================
R CMD BUILD
===============================
* checking for file ‘stPipe/DESCRIPTION’ ... OK
* preparing ‘stPipe’:
* checking DESCRIPTION meta-information ... OK
* cleaning src
* installing the package 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
* building ‘stPipe_0.99.3.tar.gz’
===============================
BiocCheckGitClone('stPipe')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe
→ BiocVersion: 3.21
→ Package: stPipe
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
! WARNING: System files in '/inst' should not be Git tracked.
• inst/.DS_Store
• ...
• inst/rmarkdown/templates/stpipe-report/skeleton/.DS_Store
✖ ERROR: System files found that should not be Git tracked.
• man/.DS_Store
• ...
• stPipe.Rproj
* Checking individual file sizes...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking if DESCRIPTION is well formatted...
* 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 v1.43.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe.Rcheck’
* using R Under development (unstable) (2025-03-13 r87965)
* 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 24.04.2 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘stPipe/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘stPipe’ version ‘0.99.3’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 26 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 ‘stPipe’ can be installed ... ERROR
Installation failed.
See ‘/home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe.Rcheck/00install.out’ for details.
* DONE
Status: 1 ERROR
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe.Rcheck/00check.log’
for details.
===============================
BiocCheck('stPipe_0.99.3.tar.gz')
===============================
── Installing stPipe ───────────────────────────────────────────────────────────
✔ Package installed successfully
── stPipe session metadata ─────────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpcKnAbo/file7056f52ebdfd2/stPipe
→ BiocVersion: 3.21
→ Package: stPipe
→ PackageVersion: 0.99.3
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3720/e271a01594fad9b572fdb92eb73ddbf0bb1ae229/stPipe.BiocCheck
→ BiocCheckVersion: 1.43.12
→ sourceDir: /tmp/RtmpcKnAbo/file7056f52ebdfd2/stPipe
→ installDir: /tmp/RtmpcKnAbo/file7056f7815d2bd
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on stPipe ─────────────────────────────────────────────────
* Checking for deprecated package usage...
* Checking for remote package usage...
* Checking for 'LazyData: true' usage...
i NOTE: 'LazyData:' in the 'DESCRIPTION' should be set to false or removed
* 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 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 (31%).
* 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 .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of stPipe...
* Checking coding practice...
i NOTE: Avoid 1:...; use seq_len() or seq_along()
Found in files:
• Run_Interactive.R (line 62, column 50)
• ...
• Run_Visualization.R (line 86, column 55)
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• print() in R/Run_Loc_Match.R (line 26, column 5)
• ...
• print() in R/Run_Visualization.R (line 25, column 5)
i NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
Found in files:
• R/Run_ST.R (line 141, column 14)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 1 times:
• T in R/Run_Create_Obj.R (line 73, column 79)
i NOTE: Avoid system() ; use system2()
Found in files:
• system() in R/Run_Loc_Match.R (line 98, column 5)
• system() in R/Run_ST.R (line 138, column 9)
* 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 10
functions greater than 50 lines.
The longest 5 functions are:
• Run_ST() (R/Run_ST.R): 246 lines
• ...
• Run_Visualization() (R/Run_Visualization.R): 100 lines
* Checking man page documentation...
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• Run_Clustering.Rd
• ...
• Run_ST.Rd
i NOTE: Usage of dontrun / donttest tags found in man page examples. 78% of man
pages use at least one of these tags.
Found in files:
• Run_Clustering.Rd
• ...
• Run_Vis.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• Run_Clustering.Rd
• ...
• Run_Vis.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; 221 lines (15%) are > 80 characters long.
First few lines:
• R/help.R#L1 #' stPipe: A package for pre-processing ...
• ...
• vignettes/stPipe-vignette.Rmd#L194 Upstream pre-processing is never the end
...
i NOTE: Consider multiples of 4 spaces for line indents; 499 lines (33%) are
not.
First few lines:
• R/basilisk.R#L3 envname = "stPipe_env", ...
• ...
• vignettes/stPipe-vignette.Rmd#L167 show.config = FALSE ...
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 v1.43.12 results ──────────────────────────────────────────────────
✖ 1 ERRORS | ⚠ 1 WARNINGS | i 12 NOTES
i See the stPipe.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.