===============================
R CMD BUILD
===============================
* checking for file ‘OSTA/DESCRIPTION’ ... OK
* preparing ‘OSTA’:
* 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
* building ‘OSTA_0.99.5.tar.gz’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/doc/book/images/seq-preprocessing-CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevF_library_construction.jpg’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/doc/book/images/seq-preprocessing-Stereo-seq_Analysis_Workflow_Manual_fastq_File_Format.png’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/doc/book/images/seq-preprocessing-Stereo_seq_Transcriptomics_Set_for_Chip_on_a_slide_User_Manual_Ver_A_Jan_2023_Transcriptome_Library_Construct.jpg’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/doc/book/site_libs/quarto-html/quarto-syntax-highlighting-c1f63da3e08f13bc72dc17e92cfd001d.css’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/images/seq-preprocessing-CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevF_library_construction.jpg’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
storing paths of more than 100 bytes is not portable:
‘OSTA/inst/images/seq-preprocessing-Stereo_seq_Transcriptomics_Set_for_Chip_on_a_slide_User_Manual_Ver_A_Jan_2023_Transcriptome_Library_Construct.jpg’
Warning in utils::tar(filepath, pkgname, compression = compression, compression_level = 9L, :
using GNU extension for long pathname
===============================
BiocCheckGitClone('OSTA')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA
→ BiocVersion: 3.22
→ Package: OSTA
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
Warning in readLines(gitignore) :
incomplete final line found on '/home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA/.gitignore'
✖ ERROR: System files found that should not be Git tracked.
• OSTA.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 v1.45.11 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/3859/OSTA_20250801104449/OSTA.Rcheck’
* using R version 4.5.1 (2025-06-13)
* 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 ‘OSTA/DESCRIPTION’ ... OK
* this is package ‘OSTA’ version ‘0.99.5’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... INFO
Imports includes 62 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 ... WARNING
Found the following files with non-portable file names:
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/estimating intensity-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/local lees l-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/local moran pvals-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/local moran-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/plot moran genes-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/plot object-1.png
inst/doc/book/pages/ind-spatial-statistics_files/figure-html/weight matrix-1.png
These are not fully portable file names.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
ERROR
Found the following non-portable file paths:
OSTA/inst/doc/book/images/seq-preprocessing-CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevF_library_construction.jpg
OSTA/inst/doc/book/images/seq-preprocessing-Stereo-seq_Analysis_Workflow_Manual_fastq_File_Format.png
OSTA/inst/doc/book/images/seq-preprocessing-Stereo_seq_Transcriptomics_Set_for_Chip_on_a_slide_User_Manual_Ver_A_Jan_2023_Transcriptome_Library_Construct.jpg
OSTA/inst/doc/book/site_libs/quarto-html/quarto-syntax-highlighting-c1f63da3e08f13bc72dc17e92cfd001d.css
OSTA/inst/images/seq-preprocessing-CG000495_VisiumCytAssist_GeneExpressionUserGuide_RevF_library_construction.jpg
OSTA/inst/images/seq-preprocessing-Stereo_seq_Transcriptomics_Set_for_Chip_on_a_slide_User_Manual_Ver_A_Jan_2023_Transcriptome_Library_Construct.jpg
Tarballs are only required to store paths of up to 100 bytes and cannot
store those of more than 256 bytes, with restrictions including to 100
bytes for the final component.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘OSTA’ can be installed ... OK
* checking installed package size ... INFO
installed size is 9.5Mb
sub-directories of 1Mb or more:
images 8.8Mb
* checking package directory ... OK
* checking for future file timestamps ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
‘doMC’
A package should be listed in only one of these fields.
* checking top-level files ... OK
* checking for left-over files ... OK
* checking index information ... OK
* checking package subdirectories ... OK
* checking whether the package can be loaded ... [0s/0s] OK
* checking whether the package can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the package can be unloaded cleanly ... [0s/0s] OK
* checking whether the namespace can be loaded with stated dependencies ... [0s/0s] OK
* checking whether the namespace can be unloaded cleanly ... [0s/0s] OK
* checking loading without being on the library search path ... [0s/0s] OK
* checking use of S3 registration ... OK
* checking line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking include directives in Makefiles ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... NONE
* 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 ... [2s/2s] OK
* DONE
Status: 1 ERROR, 1 WARNING, 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA.Rcheck/00check.log’
for details.
===============================
BiocCheck('OSTA_0.99.5.tar.gz')
===============================
── Installing OSTA ─────────────────────────────────────────────────────────────
✔ Package installed successfully
── OSTA session metadata ───────────────────────────────────────────────────────
→ sourceDir: /tmp/Rtmp2Rvk7a/file261da71002416f/OSTA
→ BiocVersion: 3.22
→ Package: OSTA
→ PackageVersion: 0.99.5
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3859/OSTA_20250801104449/OSTA.BiocCheck
→ BiocCheckVersion: 1.45.11
→ sourceDir: /tmp/Rtmp2Rvk7a/file261da71002416f/OSTA
→ installDir: /tmp/Rtmp2Rvk7a/file261da764ef8024
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on OSTA ───────────────────────────────────────────────────
* 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...
* 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...
! WARNING: Invalid BiocViews term(s):
• 'Book'
* Checking for recommended biocViews...
No man pages found.
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...
i NOTE: 'Date:' field format is not 'YYYY-MM-DD': `r date()`
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (53%).
* 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...
i NOTE: Vignette(s) found with missing chunk labels
• Found in files:
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/stub.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of OSTA...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
Error in docTypes[isInternal] <- "internal" :
invalid subscript type 'list'
Calls: BiocCheck ... BiocCheckRun -> checkManDocumentation -> checkForValueSection
Execution halted