===============================
R CMD BUILD
===============================
* checking for file ‘spbtest5/DESCRIPTION’ ... OK
* preparing ‘spbtest5’:
* 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 ‘spbtest5_0.99.4.tar.gz’
===============================
BiocCheckGitClone('spbtest5')
===============================
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5
→ BiocVersion: 3.20
→ Package: spbtest5
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5
→ installDir: NULL
→ isTarBall: FALSE
→ platform: unix
* Checking valid files...
* 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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 0 WARNINGS | • 1 NOTES
i For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5.Rcheck’
* using R version 4.4.1 (2024-06-14)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 13.2.0-23ubuntu4) 13.2.0
GNU Fortran (Ubuntu 13.2.0-23ubuntu4) 13.2.0
* running under: Ubuntu 24.04.1 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest5/DESCRIPTION’ ... OK
* this is package ‘spbtest5’ version ‘0.99.4’
* 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 serialization versions ... OK
* checking whether package ‘spbtest5’ 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 ... [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 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 ... [2s/2s] OK
* checking Rd files ... [0s/0s] OK
* checking Rd metadata ... NOTE
Rd files without \alias:
‘utils2.Rd’
* 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 ... [0s/1s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [0s/10s]
[1s/11s] 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 ... [2s/2s] OK
* DONE
Status: 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5.Rcheck/00check.log’
for details.
===============================
BiocCheck('spbtest5_0.99.4.tar.gz')
===============================
── Installing spbtest5 ─────────────────────────────────────────────────────────
✔ Package installed successfully
── spbtest5 session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpF4yU2e/file11a27534823fd4/spbtest5
→ BiocVersion: 3.20
→ Package: spbtest5
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/spbtest5_20241024114853/spbtest5.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpF4yU2e/file11a27534823fd4/spbtest5
→ installDir: /tmp/RtmpF4yU2e/file11a2754a53fa6b
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on spbtest5 ───────────────────────────────────────────────
* 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...
* 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...
i NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R' with
'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
i NOTE: Provide 'URL', 'BugReports' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i NOTE: No Bioconductor dependencies detected. Note that some infrastructure
packages may not have Bioconductor dependencies. For more information, reach
out to the Bioconductor community and/or consider a CRAN submission.
* Checking for pinned package versions in DESCRIPTION...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
! WARNING: Use RMarkdown instead of Sweave 'Rnw' vignettes.
Rnw vignette(s) found:
• spbtest5.Rnw
• test.Rnw
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• test3.Rmd (code line 8, column 18)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found in files:
• vignettes/test.Rnw (code line 8, column 13)
i NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
• vignettes/spbtest5.Rnw
• ...
• vignettes/test3.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest5...
* Checking coding practice...
i NOTE: Avoid 'cat' and 'print' outside of 'show' methods
Found in files:
• cat() in R/new_test.R (line 2, column 9)
• cat() in R/test.R (line 3, column 5)
• print() in R/utils.R (line 5, column 5)
i NOTE: Avoid using '=' for assignment and use '<-' instead
Found in files:
• R/utils.R (line 9, column 8)
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 5 times:
• T in R/test.R (line 21, column 10)
• ...
• T in R/utils.R (line 2, column 16)
! WARNING: Avoid class membership checks with class() / is() and == / !=; Use
is(x, 'class') for S4 classes
Found in files:
• utils.R (line 10, column 14)
! WARNING: Remove set.seed usage (found 1 times)
• set.seed() in R/test.R (line 38, column 5)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* Checking man page documentation...
i NOTE: Usage of dontrun / donttest tags found in man page examples. 67% of man
pages use at least one of these tags.
Found in files:
• test.Rd
• utils.Rd
i NOTE: Use donttest instead of dontrun.
Found in files:
• utils.Rd
* Checking package NEWS...
i NOTE: Consider adding a NEWS file, so your package news will be included in
Bioconductor release announcements.
* Checking unit tests...
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain tabs.
First few lines:
• R/new_test.R#L2 cat("This is x",x) ...
• R/new_test.R#L3 x + 2 ...
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 v1.41.17 results ──────────────────────────────────────────────────
✖ 0 ERRORS | ⚠ 6 WARNINGS | • 10 NOTES
i See the spbtest5.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.