===============================
R CMD BUILD
===============================
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* preparing ‘spbtest3’:
* 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 ‘spbtest3_0.99.113.tar.gz’
===============================
BiocCheckGitClone('spbtest3')
===============================
This is BiocCheckGitClone version 1.29.8. BiocCheckGitClone is a work
in progress. Output and severity of issues may change.
* Checking valid files...
* Checking DESCRIPTION...
* Checking if DESCRIPTION is well formatted...
* Checking for valid maintainer...
* ERROR: Use Authors@R field not Author/Maintainer fields. Do not
use both.
* Checking CITATION...
Summary:
ERROR count: 1
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheckGitClone FAILED.
===============================
R CMD CHECK
===============================
* using log directory ‘/home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20210618090628/spbtest3.Rcheck’
* using R version 4.1.0 beta (2021-05-03 r80259)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘spbtest3/DESCRIPTION’ ... OK
* this is package ‘spbtest3’ version ‘0.99.113’
* 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 serialization versions ... OK
* checking whether package ‘spbtest3’ can be installed ... [1s/1s] 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 ... 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 ... [2s/2s] 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 ... WARNING
Undocumented arguments in documentation object 'test'
‘x’
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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [0s/1s] 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: 1 WARNING
See
‘/home/pkgbuild/packagebuilder/workers/jobs/51/spbtest3_20210618090628/spbtest3.Rcheck/00check.log’
for details.
===============================
BiocCheck('spbtest3_0.99.113.tar.gz')
===============================
This is BiocCheck version 1.29.8. BiocCheck is a work in progress.
Output and severity of issues may change. 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...
* WARNING: Description field in the DESCRIPTION file is too concise
* 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 DESCRIPTION/NAMESPACE consistency...
* Checking .Rbuildignore...
* Checking vignette directory...
* NOTE: 'sessionInfo' not found in vignette(s)
Missing from file(s):
spbtest3.Rnw
test.Rnw
test2.Rmd
test3.Rmd
test4.Rmd
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of spbtest3...
* Checking coding practice...
* WARNING: Use TRUE/FALSE instead of T/F
Found in R/ directory functions:
test4()
Found in files:
inst/doc/test.R
inst/doc/test.Rnw
vignettes/test.Rnw
* WARNING: Avoid class() == or class() != ; use is() or !is()
Found in files:
R/utils.R (line 10)
vignettes/test3.Rmd (line 23)
* WARNING: Remove set.seed usage in R code
Found in R/ directory functions:
test7()
* Checking parsed R code in R directory, examples, vignettes...
* Checking function lengths...........
* Checking man page documentation...
* NOTE: Usage of dontrun{} / donttest{} found in man page examples.
67% of man pages use one of these cases.
Found in the following files:
test.Rd
utils.Rd
* NOTE: Use donttest{} instead of dontrun{}.
Found in the following files:
utils.Rd
* Checking package NEWS...
* NOTE: Consider adding a NEWS file, so your package news will be
included in Bioconductor release announcements.
* Checking unit tests...
* NOTE: Consider adding unit tests. We strongly encourage them. See
http://bioconductor.org/developers/how-to/unitTesting-guidelines/.
* Checking skip_on_bioc() in tests...
* Checking formatting of DESCRIPTION, NAMESPACE, man pages, R source,
and vignette source...
* NOTE: Consider shorter lines; 1 lines (0%) are > 80 characters
long.
First 1 lines:
man/test.Rd:12 A simple test function. \code{\link{show}} \code{lin...
* NOTE: Consider 4 spaces instead of tabs; 2 lines (1%) contain
tabs.
First 2 lines:
R/new_test.R:2 cat("This is x",x)
R/new_test.R:3 x + 2
* NOTE: Consider multiples of 4 spaces for line indents, 7
lines(3%) are not.
First 6 lines:
man/test.Rd:25 # test a donttest
man/test.Rd:26 me <- "lori"
man/utils.Rd:19 # test a dontrun
man/utils.Rd:20 a = 1
vignettes/test2.Rmd:5 BiocStyle::html_document:
vignettes/test3.Rmd:5 BiocStyle::html_document:
See http://bioconductor.org/developers/how-to/coding-style/
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.
* ERROR: Maintainer must add package name to Watched Tags on the
support site; Edit your Support Site User Profile to add Watched
Tags.
Summary:
ERROR count: 1
WARNING count: 4
NOTE count: 8
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.14/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
BiocCheck FAILED.