===============================
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/ea2e33927da530010d994f09fc38f4a45e0196bc/spbtest5
→ BiocVersion: 3.20
→ Package: spbtest5
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/ea2e33927da530010d994f09fc38f4a45e0196bc/spbtest5.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/ea2e33927da530010d994f09fc38f4a45e0196bc/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/ea2e33927da530010d994f09fc38f4a45e0196bc/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 ... WARNING
Undocumented arguments in Rd file 'test.Rd'
‘x’
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 WARNING, 1 NOTE
See
‘/media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/ea2e33927da530010d994f09fc38f4a45e0196bc/spbtest5.Rcheck/00check.log’
for details.
===============================
BiocCheck('spbtest5_0.99.4.tar.gz')
===============================
── Installing spbtest5 ─────────────────────────────────────────────────────────
✔ Package installed successfully
── spbtest5 session metadata ───────────────────────────────────────────────────
→ sourceDir: /tmp/RtmpJvhraM/file306ffe1f23bc6b/spbtest5
→ BiocVersion: 3.20
→ Package: spbtest5
→ PackageVersion: 0.99.4
→ BiocCheckDir: /media/volume/teran2_disk/pkgbuild/packagebuilder/workers/jobs/3145/ea2e33927da530010d994f09fc38f4a45e0196bc/spbtest5.BiocCheck
→ BiocCheckVersion: 1.41.17
→ sourceDir: /tmp/RtmpJvhraM/file306ffe1f23bc6b/spbtest5
→ installDir: /tmp/RtmpJvhraM/file306ffef494d8
→ 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.