===============================
R CMD BUILD
===============================
* checking for file ‘katdetectr/DESCRIPTION’ ... OK
* preparing ‘katdetectr’:
* checking DESCRIPTION meta-information ... OK
Warning: /tmp/RtmpZSvsXc/Rbuild35b65e4a5d2be0/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
* installing the package to process help pages
Loading required namespace: katdetectr
* saving partial Rd database
* creating vignettes ... OK
* checking for LF line-endings in source and make files and shell scripts
* checking for empty or unneeded directories
* building ‘katdetectr_0.99.5.tar.gz’
===============================
BiocCheckGitClone('katdetectr')
===============================
─ BiocCheckVersion: 1.33.9
─ BiocVersion: 3.16
─ Package: katdetectr
─ PackageVersion: 0.99.5
─ sourceDir: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr
─ 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...
─ 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/2676/katdetectr_20220623134712/katdetectr.Rcheck’
* using R version 4.2.0 Patched (2022-06-02 r82447)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘katdetectr/DESCRIPTION’ ... OK
* this is package ‘katdetectr’ 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 ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package ‘katdetectr’ can be installed ... WARNING
Found the following significant warnings:
Warning: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
See ‘/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.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 R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* checking whether the package can be loaded ... OK
* checking whether the package can be loaded with stated dependencies ... OK
* checking whether the package can be unloaded cleanly ... OK
* checking whether the namespace can be loaded with stated dependencies ... OK
* checking whether the namespace can be unloaded cleanly ... OK
* checking loading without being on the library search path ... 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 ... [26s/26s] OK
* checking Rd files ... [9s/9s] WARNING
prepare_Rd: ./man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
* 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 ... [24s/24s] OK
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘testthat.R’ [23s/21s]
[23s/21s] 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 ... OK
* DONE
Status: 2 WARNINGs
See
‘/home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.Rcheck/00check.log’
for details.
===============================
BiocCheck('katdetectr_0.99.5.tar.gz')
===============================
─ BiocCheckVersion: 1.33.9
─ BiocVersion: 3.16
─ Package: katdetectr
─ PackageVersion: 0.99.5
─ sourceDir: /tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr
─ installDir: /tmp/RtmpbYZllB/file35bdac1de858f2
─ BiocCheckDir: /home/pkgbuild/packagebuilder/workers/jobs/2676/katdetectr_20220623134712/katdetectr.BiocCheck
─ platform: unix
─ isTarBall: TRUE
* Installing package...
* Checking package dependencies...
* Checking if other packages can import this one...
* Checking to see if we understand object initialization...
* 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...
* 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 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...
Warning in tools::parse_Rd(infile) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(infile) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
* Checking for library/require of katdetectr...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...
* NOTE: The recommended function length is 50 lines or less. There
are 70 functions greater than 50 lines.
* Checking man page documentation...
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:34: unexpected VERBLATEX '\href', expecting '{'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:45: unknown macro '\insertCite'
Warning in tools::parse_Rd(manpage) :
/tmp/RtmpbYZllB/file35bdac65a9ec3d/katdetectr/man/detectKataegis.Rd:55: unknown macro '\insertRef'
* 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; 249 lines (13%) are > 80 characters
long.
* NOTE: Consider multiples of 4 spaces for line indents; 26 lines
(1%) 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 | 3 NOTES
See the katdetectr.BiocCheck folder and run
browseVignettes(package = 'BiocCheck')
for details.