===============================
R CMD BUILD
===============================
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* preparing ‘seqpac’:
* 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
Omitted ‘LazyData’ from DESCRIPTION
* building ‘seqpac_0.99.18.tar.gz’
===============================
BiocCheckGitClone('seqpac')
===============================
─ BiocCheckVersion: 1.35.2
─ BiocVersion: 3.17
─ Package: seqpac
─ PackageVersion: 0.99.18
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2275/70233391894c4c165e4c866864afdcceda747ad6/seqpac
─ platform: unix
─ isTarBall: FALSE
* Checking valid files...
* Checking for stray BiocCheck output folders...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 0 NOTES
For more details, run
browseVignettes(package = 'BiocCheck')
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/2275/70233391894c4c165e4c866864afdcceda747ad6/seqpac.Rcheck’
* using R Under development (unstable) (2022-10-25 r83175)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘seqpac/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘seqpac’ version ‘0.99.18’
* 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘seqpac’ 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 ... [2s/2s] OK
* checking whether the package can be loaded with stated dependencies ... [1s/1s] OK
* checking whether the package can be unloaded cleanly ... [1s/1s] OK
* checking whether the namespace can be loaded with stated dependencies ... [1s/1s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... [15s/15s] 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 ... [504s/484s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
make_counts 116.936 0.401 153.381
make_PAC 43.557 2.153 37.814
make_pheno 41.454 2.076 36.397
PAC_deseq 37.834 5.462 29.815
make_trim 37.977 0.089 38.067
PAC_gtf 28.300 2.428 18.039
PAC_covplot 12.267 0.329 12.595
PAC_trna 7.202 3.611 8.916
names 8.058 2.215 8.846
overview 7.905 2.090 8.588
full 7.466 1.903 8.015
simplify_reanno 7.771 1.423 8.097
tRNA_class 3.616 4.693 5.695
make_reanno 6.938 1.368 7.427
PAC_pca 7.748 0.061 7.810
map_reanno 6.369 1.277 6.750
PAC_jitter 7.500 0.136 7.636
add_reanno 6.299 0.978 6.501
map_rangetype 3.094 4.065 4.894
PAC_nbias 7.009 0.016 7.025
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [14s/14s]
[14s/14s] OK
* checking for unstated dependencies in vignettes ... OK
* checking package vignettes in ‘inst/doc’ ... 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: OK
===============================
BiocCheck('seqpac_0.99.18.tar.gz')
===============================
─ BiocCheckVersion: 1.35.2
─ BiocVersion: 3.17
─ Package: seqpac
─ PackageVersion: 0.99.18
─ sourceDir: /tmp/Rtmpeka9yK/file2193a96c1cac17/seqpac
─ installDir: /tmp/Rtmpeka9yK/file2193a9e0223d2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2275/70233391894c4c165e4c866864afdcceda747ad6/seqpac.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...
* NOTE: Update R version dependency from 4.2.0 to 4.3.0.
* Checking package size...
* Checking individual file sizes...
* Checking biocViews...
* Checking that biocViews are present...
* Checking package type based on biocViews...
Workflow
* 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...
* Checking for whitespace in DESCRIPTION field names...
* Checking that Package field matches directory/tarball name...
* Checking for Version field...
* Checking for valid maintainer...
* NOTE: Consider adding the maintainer's ORCID iD in 'Authors@R'
with 'comment=c(ORCID="...")'
* Checking License: for restrictive use...
* Checking for pinned package versions...
* Checking DESCRIPTION/NAMESPACE consistency...
* 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 seqpac...
* Checking coding practice...
* NOTE: Avoid 1:...; use seq_len() or seq_along()
* NOTE: Avoid 'cat' and 'print' outside of 'show' methods
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 270 functions greater than 50 lines.
* Checking man page documentation...
* Checking package NEWS...
* 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; 9 lines (0%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 5135 lines
(27%) 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 name is in support site watched tags.
─ BiocCheck results ──
0 ERRORS | 0 WARNINGS | 7 NOTES
See the seqpac.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.