===============================
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
* looking to see if a data/datalist file should be added
* building probeSNPffer_0.99.7.tar.gz
===============================
BiocCheckGitClone('probeSNPffer')
===============================
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/probeSNPffer
BiocVersion: 3.21
Package: probeSNPffer
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/probeSNPffer.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/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/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/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 0.99.7
* 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 ... WARNING
Found the following significant warnings:
Warning: check.for.cc.switch.Rd: Only one \usage section is allowed: the first will be used
See /home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/probeSNPffer.Rcheck/00install.out for details.
* 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 ... [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 ... [2s/2s] OK
* checking whether the namespace can be unloaded cleanly ... [2s/2s] OK
* checking loading without being on the library search path ... [2s/2s] OK
* checking use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Package in Depends field not imported from: GenomicRanges
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 ... [6s/6s] OK
* checking Rd files ... [0s/0s] WARNING
prepare_Rd: check.for.cc.switch.Rd: Only one \usage section is allowed: the first will be used
* checking Rd metadata ... OK
* checking Rd line widths ... OK
* checking Rd cross-references ... OK
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from Rd file 'check.for.cc.switch.Rd':
check.for.cc.switch
Code: function(DAT)
Docs: function(x)
Argument names in code not in docs:
DAT
Argument names in docs not in code:
x
Mismatches in argument names:
Position: 1 Code: DAT Docs: x
Codoc mismatches from Rd file 'flag.overlap.Rd':
flag.overlap
Code: function(probe_bed, SNP_bed)
Docs: function(CpG_probe_bed, SNP_bed)
Argument names in code not in docs:
probe_bed
Argument names in docs not in code:
CpG_probe_bed
Mismatches in argument names:
Position: 1 Code: probe_bed Docs: CpG_probe_bed
* checking Rd \usage sections ... WARNING
Undocumented arguments in Rd file 'check.for.cc.switch.Rd'
x
Documented arguments not in \usage in Rd file 'check.for.cc.switch.Rd':
DAT
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 ... OK
* checking data for non-ASCII characters ... [0s/0s] 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: 4 WARNINGs, 1 NOTE
See
/home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/probeSNPffer.Rcheck/00check.log
for details.
===============================
BiocCheck('probeSNPffer_0.99.7.tar.gz')
===============================
Installing probeSNPffer
Package installed successfully
probeSNPffer session metadata
sourceDir: /tmp/RtmpyX9nbx/file3ee5da41c74e10/probeSNPffer
BiocVersion: 3.21
Package: probeSNPffer
PackageVersion: 0.99.7
BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3610/02fd3aeb55c0a781c63398eca18c02b1b7868dfc/probeSNPffer.BiocCheck
BiocCheckVersion: 1.43.2
sourceDir: /tmp/RtmpyX9nbx/file3ee5da41c74e10/probeSNPffer
installDir: /tmp/RtmpyX9nbx/file3ee5da46b2fff6
isTarBall: TRUE
platform: unix
Running BiocCheck on probeSNPffer
* 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...
i NOTE: Update R version dependency from 4.4.0 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...
* 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 (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...
Warning: check.for.cc.switch.Rd: Only one \usage section is allowed: the first will be used
* Checking for library/require of probeSNPffer...
* Checking coding practice...
! WARNING: Avoid T/F variables; If logical, use TRUE/FALSE
Found 3 times:
T in R/extract_probe_regions.R (line 24, column 63)
T in R/flag_overlap.R (line 6, column 65)
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; 66 lines (15%) 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#L175 legend.position =
"none") + scal ...
i NOTE: Consider multiples of 4 spaces for line indents; 108 lines (25%) are
not.
First few lines:
R/calc_probe_coords.R#L4 strand <- DAT[4] ...
...
vignettes/identifying_probe_SNPs_introduction.Rmd#L173 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 6 NOTES
i See the probeSNPffer.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.