===============================
R CMD BUILD
===============================
* checking for file ‘probeSNPffer/DESCRIPTION’ ... OK
* preparing ‘probeSNPffer’:
* 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 ‘probeSNPffer_0.99.0.tar.gz’
===============================
BiocCheckGitClone('probeSNPffer')
===============================
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/probeSNPffer_20241127194121/probeSNPffer
→ BiocVersion: 3.21
→ Package: probeSNPffer
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/probeSNPffer_20241127194121/probeSNPffer.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/probeSNPffer_20241127194121/probeSNPffer
→ 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 v1.43.2 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/3610/probeSNPffer_20241127194121/probeSNPffer.Rcheck’
* using R Under development (unstable) (2024-10-21 r87258)
* 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 ‘probeSNPffer/DESCRIPTION’ ... OK
* this is package ‘probeSNPffer’ version ‘0.99.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ...Warning: unable to access index for repository https://CRAN.R-project.org/src/contrib:
cannot open URL 'https://CRAN.R-project.org/src/contrib/PACKAGES'
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 whether package ‘probeSNPffer’ 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 ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
‘GenomicRanges’ ‘S4Vectors’
A package should be listed in only one of these fields.
'LinkingTo' field is unused: package has no 'src' directory
* 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
* checking whether the package can be unloaded cleanly ... [2s/2s] 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 ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'::' or ':::' import not declared from: ‘IRanges’
Packages in Depends field not imported from:
‘BiocGenerics’ ‘GenomicRanges’ ‘S4Vectors’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* 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 ... OK
* checking Rd line widths ... NOTE
Rd file 'calc.probe.coords.Rd':
\usage lines wider than 90 characters:
bed_file[,c("start", "end")] <- t(apply(X=manifest_anno_object, MARGIN=1, FUN=calc.probe.coords))
Rd file 'check.for.cc.switch.Rd':
\usage lines wider than 90 characters:
probe_SNP_info$col_chan_switching <- apply(X=probe_SNP_info, MARGIN=1, FUN=check.for.cc.switch)
These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
‘CpG_info’ ‘SNP_bed’
Undocumented data sets:
‘CpG_info’ ‘SNP_bed’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'extract.probe.regions.Rd':
extract.probe.regions
Code: function(manifest_anno_object)
Docs: function(manifest_anno_object = CpG_info)
Mismatches in argument default values:
Name: 'manifest_anno_object' Code: Docs: CpG_info
Codoc mismatches from Rd file 'flag.overlap.Rd':
flag.overlap
Code: function(probe_bed, SNP_bed)
Docs: function(probe_bed = CpG_probe_bed, SNP_bed = SNP_bed[, 1:6])
Mismatches in argument default values:
Name: 'probe_bed' Code: Docs: CpG_probe_bed
Name: 'SNP_bed' Code: Docs: SNP_bed[, 1:6]
* checking Rd \usage sections ... WARNING
Assignments in \usage in Rd file 'calc.probe.coords.Rd':
bed_file[, c("start", "end")] <- t(apply(X = manifest_anno_object,
MARGIN = 1, FUN = calc.probe.coords))
Assignments in \usage in Rd file 'check.for.cc.switch.Rd':
probe_SNP_info$col_chan_switching <- apply(X = probe_SNP_info,
MARGIN = 1, FUN = check.for.cc.switch)
Undocumented arguments in Rd file 'extract.probe.regions.Rd'
‘manifest_anno_object’
Undocumented arguments in Rd file 'flag.overlap.Rd'
‘probe_bed’ ‘SNP_bed’
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 contents of ‘data’ directory ... WARNING
Files not of a type allowed in a ‘data’ directory:
‘DATA_info’
Please use e.g. ‘inst/extdata’ for non-R data files
* checking data for non-ASCII characters ... [0s/0s] OK
* checking LazyData ... OK
* checking data for ASCII and uncompressed saves ... 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 ... [3s/3s] OK
* DONE
Status: 5 WARNINGs, 2 NOTEs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3610/probeSNPffer_20241127194121/probeSNPffer.Rcheck/00check.log’
for details.
===============================
BiocCheck('probeSNPffer_0.99.0.tar.gz')
===============================
── Installing probeSNPffer ─────────────────────────────────────────────────────
✔ Package installed successfully
── probeSNPffer session metadata ───────────────────────────────────────────────
→ sourceDir: /tmp/RtmpAg23Xk/file3b1c844d540485/probeSNPffer
→ BiocVersion: 3.21
→ Package: probeSNPffer
→ PackageVersion: 0.99.0
→ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/probeSNPffer_20241127194121/probeSNPffer.BiocCheck
→ BiocCheckVersion: 1.43.2
→ sourceDir: /tmp/RtmpAg23Xk/file3b1c844d540485/probeSNPffer
→ installDir: /tmp/RtmpAg23Xk/file3b1c843a336dd2
→ isTarBall: TRUE
→ platform: unix
── Running BiocCheck on probeSNPffer ───────────────────────────────────────────
* 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 3.5.0 to 4.5.0.
* 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...
i NOTE: Consider adding these automatically suggested biocViews:
MethylationArray
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...
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' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
i Bioconductor dependencies found in Imports & Depends (100%).
* Checking for pinned package versions in DESCRIPTION...
* 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 probeSNPffer...
* Checking coding practice...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 8 times:
• T in R/check_for_cc_switch.R (line 14, column 16)
• ...
• T in R/flag_overlap.R (line 9, column 61)
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
i NOTE: The recommended function length is 50 lines or less. There is 1
function greater than 50 lines.
The longest 5 functions are:
• extract.probe.regions() (R/extract_probe_regions.R): 51 lines
* Checking man page documentation...
! WARNING: Empty or missing \value sections found in man page(s).
Found in files:
• man/calc.probe.coords.Rd
• ...
• man/flag.overlap.Rd
✖ ERROR: At least 80% of man pages documenting exported objects must have
runnable examples.
The following pages do not:
• calc.probe.coords.Rd
• ...
• flag.overlap.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...
i NOTE: Consider adding unit tests. We strongly encourage them. See
https://contributions.bioconductor.org/tests.html
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source, and
vignette source...
i NOTE: Consider shorter lines; 57 lines (16%) are > 80 characters long.
First few lines:
• R/check_for_cc_switch.R#L11 if ((ref == 'A' & alt == 'T') | (r ...
• ...
• vignettes/identifying_probe_SNPs_introduction.Rmd#L171 legend.position =
"none") + scal ...
i NOTE: Consider multiples of 4 spaces for line indents; 96 lines (27%) are
not.
First few lines:
• R/calc_probe_coords.R#L4 strand <- DAT[4] ...
• ...
• vignettes/identifying_probe_SNPs_introduction.Rmd#L169 theme(panel.grid.major
= element_blank ...
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...
✖ ERROR: Subscribe to the Bioc-devel mailing list by going to
https://stat.ethz.ch/mailman/listinfo/bioc-devel
* Checking for support site registration...
✖ ERROR: Unable to find your email in the Support Site: HTTP 404 Not Found.
── BiocCheck v1.43.2 results ───────────────────────────────────────────────────
✖ 3 ERRORS | ⚠ 2 WARNINGS | i 10 NOTES
i See the probeSNPffer.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.