Package: vulcan

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vulcan_1.4.0.tar.gz

StartedAt: 2019-04-16 03:21:17 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 03:27:24 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 367.7 seconds

RetCode: 0

Status:  OK

CheckDir: vulcan.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:vulcan.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings vulcan_1.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/vulcan.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘vulcan/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘vulcan’ version ‘1.4.0’
* package encoding: UTF-8
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘ChIPpeakAnno’ ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘zoo’
  ‘GenomicRanges’ ‘S4Vectors’ ‘viper’ ‘DiffBind’ ‘locfit’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘vulcan’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... 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 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
average_fragment_length 6.334   0.29   6.677
* 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 NOTE
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/vulcan.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL vulcan
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘vulcan’ ...
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (vulcan)

name	user	system	elapsed
average_fragment_length	6.334	0.290	6.677
corr2p	0.001	0.001	0.002
densityauc	0.029	0.004	0.034
dpareto	0.003	0.000	0.004
fisherp	0.000	0.001	0.000
gsea	0.973	0.065	1.039
kmgformat	0.011	0.002	0.013
null_gsea	0.034	0.004	0.038
p2corr	0	0	0
p2z	0.000	0.000	0.001
pareto.fit	0.007	0.001	0.008
plot_gsea	0.037	0.002	0.039
ppareto	0.004	0.000	0.004
rea	0.003	0.000	0.003
slice	0.000	0.000	0.001
stouffer	0	0	0
textplot2	0.233	0.025	0.258
val2col	0.005	0.000	0.004
vulcan	2.806	0.183	3.011
vulcan.annotate	1.356	0.069	1.428
vulcan.import	0.019	0.001	0.021
vulcan.normalize	0	0	0
vulcan.pathways	1.636	0.109	1.747
wstouffer	0	0	0
z2p	0.000	0.001	0.001