===============================
R CMD BUILD
===============================
* checking for file ‘beer/DESCRIPTION’ ... OK
* preparing ‘beer’:
* 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 ‘beer_0.99.3.tar.gz’
===============================
BiocCheckGitClone('beer')
===============================
This is BiocCheckGitClone version 1.31.31. 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...
* Checking CITATION...
* Checking that provided CITATION file is correctly formatted...
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 0
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD CHECK
===============================
* using log directory ‘/Users/pkgbuild/packagebuilder/workers/jobs/2500/0c674bc06195a219a3f97992403d775864e6ec24/beer.Rcheck’
* using R Under development (unstable) (2022-01-05 r81451)
* using platform: x86_64-apple-darwin17.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘beer/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘beer’ version ‘0.99.3’
* 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 ‘beer’ can be installed ... [38s/39s] 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 ... [40s/43s] OK
* checking Rd files ... [1s/1s] 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [296s/337s] OK
Examples with CPU (user + system) or elapsed time > 5s
user system elapsed
brew 177.224 5.630 238.416
beadsRR 68.690 6.270 39.609
brewOne 14.176 0.427 14.693
runEdgeR 4.783 0.524 26.302
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘spelling.R’ [0s/1s]
Running ‘testthat.R’ ERROR
TIMEOUT: R CMD check exceeded 14 mins
===============================
BiocCheck('beer_0.99.3.tar.gz')
===============================
This is BiocCheck version 1.31.31. BiocCheck is a work in progress.
Output and severity of issues may change. Installing package...
* Checking Package Dependencies...
Warning in system2(cmd, args, stdout = TRUE, stderr = FALSE, env = "R_DEFAULT_PACKAGES=NULL") :
running command 'R_DEFAULT_PACKAGES=NULL '/Library/Frameworks/R.framework/Resources/bin/R' -q --vanilla --slave -f /Library/Frameworks/R.framework/Versions/4.2/Resources/library/BiocCheck/script/checkBadDeps.R --args "/Users/pkgbuild/packagebuilder/workers/jobs/2500/0c674bc06195a219a3f97992403d775864e6ec24/beer_0.99.3.tar.gz" "/var/folders/7y/c__3_48d5y18p1_rhfs_4x9c0000gt/T//RtmpBwtYSY/file18298410cdb6c/lib" 2>/dev/null' had status 1
* 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 vignette directory...
* Checking whether vignette is built with 'R CMD build'...
* Checking package installation calls in R code...
* Checking for library/require of beer...
* Checking coding practice...
* Checking parsed R code in R directory, examples, vignettes...
* NOTE: Avoid 'suppressWarnings'/'*Messages' if possible (found 1
times)
suppressMessages() in R/edgeR.R (line 30, column 20)
* Checking function lengths...
* NOTE: Recommended function length <= 50 lines.
There are 9 functions > 50 lines.
The longest 5 functions are:
brew() (R/brew.R, line 458): 144 lines
.beadsRRBeer() (R/beadsRR.R, line 25): 129 lines
summarizeRun() (R/summarizeRun.R, line 96): 98 lines
runEdgeR() (R/edgeR.R, line 121): 92 lines
.brewSamples() (R/brew.R, line 290): 57 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; 60 lines (2%) are > 80 characters
long.
First 6 lines:
R/beadsRR.R:134 out <- summarizeRun(object, file.path(tmp.dir, ...
R/guessInits.R:27 #' @seealso \emph{Methods} in [Chen et. al 2022](http...
man/beer-package.Rd:7 \title{beer: an R package for quantifying antibod...
man/beer-package.Rd:22 \strong{Maintainer}: Athena Chen \email{achen70@...
man/brew.Rd:9 prior.params = list(method = "edgeR", a_pi = 2, b_pi = ...
man/brew.Rd:13 jags.params = list(n.chains = 1, n.adapt = 1000, n.ite...
* NOTE: Consider multiples of 4 spaces for line indents, 169
lines(5%) are not.
First 6 lines:
R/brew.R:93 se.params$beads.prior <- beads.prior
R/brew.R:94 }
man/beer-package.Rd:16 \item \url{https://github.com/athchen/beer/}
man/beer-package.Rd:17 \item Report bugs at \url{https://github.com/a...
man/beer-package.Rd:26 \item Rob Scharpf \email{rscharpf@jhu.edu}
man/beer-package.Rd:27 \item Ingo Ruczinski \email{ingo@jhu.edu}
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.
Package name is in support site watched tags.
Summary:
ERROR count: 0
WARNING count: 0
NOTE count: 4
For detailed information about these checks, see the BiocCheck
vignette, available at
https://bioconductor.org/packages/3.15/bioc/vignettes/BiocCheck/inst/doc/BiocCheck.html#interpreting-bioccheck-output
===============================
R CMD BUILD
===============================
>>>>>>>
>>>>>>> INSTALLATION WITH 'R CMD INSTALL --preclean --no-multiarch --library=libdir beer_0.99.3.tar.gz'
>>>>>>>
* installing *source* package ‘beer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
*** copying figures
** building package indices
** installing vignettes
** testing if installed package can be loaded from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (beer)
===============================
R CMD BUILD
===============================
* checking for file ‘beer/DESCRIPTION’ ... OK
* preparing ‘beer’:
* checking DESCRIPTION meta-information ... OK
* installing the package to build vignettes
-----------------------------------
* installing *source* package ‘beer’ ...
** using staged installation
** R
** inst
** byte-compile and prepare package for lazy loading
Error: package or namespace load failed for ‘PhIPData’:
.onLoad failed in loadNamespace() for 'PhIPData', details:
call: gzfile(file, "wb")
error: cannot open the connection
In addition: Warning message:
In gzfile(file, "wb") :
cannot open compressed file '/home/biocbuild/bbs-3.15-bioc/R/library/PhIPData/extdata/defaults.rda', probable reason 'Permission denied'
Execution halted
ERROR: lazy loading failed for package ‘beer’
* removing ‘/tmp/RtmpXTbJIH/Rinstb1fc242b8a5b0/beer’
-----------------------------------
ERROR: package installation failed