===============================
R CMD BUILD
===============================
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* preparing ‘ginmappeR’:
* 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 ‘ginmappeR_0.99.5.tar.gz’
===============================
BiocCheckGitClone('ginmappeR')
===============================
─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/3124/b0ddc017fc575a41e75e947f0a21d7da3c67328b/ginmappeR
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking for inst/doc folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* NOTE: No CITATION file found. Bioconductor packages are not
required to have a CITATION file but it is useful both for users
and for tracking Bioconductor project-wide metrics. If you later
post a preprint or publish a paper about your Bioconductor
package, please add the details with a 'doi' argument in the
CITATION file's 'bibentry()'.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 1 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/3124/b0ddc017fc575a41e75e947f0a21d7da3c67328b/ginmappeR.Rcheck’
* using R Under development (unstable) (2024-01-16 r85808)
* using platform: x86_64-pc-linux-gnu
* R was compiled by
gcc (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
GNU Fortran (Ubuntu 11.4.0-1ubuntu1~22.04) 11.4.0
* running under: Ubuntu 22.04.3 LTS
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ginmappeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ginmappeR’ version ‘0.99.5’
* package encoding: UTF-8
* 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 ... NOTE
Found the following hidden files and directories:
.BBSoptions
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘ginmappeR’ 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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... [5s/5s] OK
* checking whether the package can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the package can be unloaded cleanly ... [4s/4s] OK
* checking whether the namespace can be loaded with stated dependencies ... [5s/5s] OK
* checking whether the namespace can be unloaded cleanly ... [5s/5s] OK
* checking loading without being on the library search path ... [5s/5s] OK
* checking whether startup messages can be suppressed ... [5s/5s] 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 ... [19s/19s] OK
* checking Rd files ... [0s/0s] OK
* 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 ... OK
* checking Rd \usage sections ... OK
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/337s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
getCARD2KEGG 2.059 0.120 21.295
getUniProt2NCBIGene 1.845 0.061 26.532
getNCBIGene2CARD 1.250 0.083 65.802
getCARD2UniProt 1.151 0.048 12.489
getNCBINucleotide2KEGG 1.143 0.040 25.039
getKEGG2NCBINucleotide 0.914 0.020 12.832
getNCBIProtein2UniProt 0.809 0.005 15.109
getNCBIGene2KEGG 0.626 0.033 11.400
getCARD2NCBIGene 0.613 0.016 39.063
getUniProt2KEGG 0.544 0.016 9.226
getUniProt2NCBIProtein 0.429 0.008 7.328
getKEGG2NCBIGene 0.427 0.004 7.194
getNCBIProtein2KEGG 0.402 0.012 13.677
getUniProt2NCBINucleotide 0.348 0.012 6.958
getNCBINucleotide2UniProt 0.345 0.012 5.247
getNCBIGene2UniProt 0.270 0.000 5.507
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘runTests.R’ [26s/358s]
[26s/358s] 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 ... [4s/4s] OK
* DONE
Status: 1 NOTE
See
‘/home/pkgbuild/packagebuilder/workers/jobs/3124/b0ddc017fc575a41e75e947f0a21d7da3c67328b/ginmappeR.Rcheck/00check.log’
for details.
WARNING: R CMD check exceeded 10 min requirement
===============================
BiocCheck('ginmappeR_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.39.21
─ BiocVersion: 3.19
─ Package: ginmappeR
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpzaS60f/file221f695c5cf0b8/ginmappeR
─ installDir: /tmp/RtmpzaS60f/file221f696cb28350
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/3124/b0ddc017fc575a41e75e947f0a21d7da3c67328b/ginmappeR.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* 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 blank lines in DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for proper Description: field...
* NOTE: The Description field in the DESCRIPTION is made up by less
than 3 sentences. Please consider expanding this field, and
structure it as a full paragraph
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version: field...
* Checking for valid maintainer...
* Checking License: for restrictive use...
* Checking for recommended DESCRIPTION fields...
* NOTE: Provide 'URL', 'BugReports', 'Date' field(s) in DESCRIPTION
* Checking for Bioconductor software dependencies...
Bioconductor dependencies found in Imports & Depends (25%).
* Checking for pinned package versions in DESCRIPTION...
* Checking DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking for stray BiocCheck output folders...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of ginmappeR...
* Checking coding practice...
* NOTE: Avoid sapply(); use vapply()
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid using '=' for assignment and use '<-' instead
* NOTE: Avoid redundant 'stop' and 'warn*' in signal conditions
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid '<<-' if possible (found 31 times)
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 29
times)
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 4 functions greater than 50 lines.
* Checking man page documentation...
* NOTE: Consider adding runnable examples to man pages that
document exported objects.
* Checking package NEWS...
* 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...
* NOTE: Consider shorter lines; 374 lines (11%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 299 lines
(9%) are not.
See https://contributions.bioconductor.org/r-code.html
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...
Maintainer is subscribed to bioc-devel.
* Checking for support site registration...
Maintainer is registered at support site.
Package is in the Support Site Watched Tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 14 NOTES
See the ginmappeR.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.