Package: vulcan

Version: 1.5.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings vulcan_1.5.0.tar.gz

StartedAt: 2019-04-09 04:17:51 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 04:23:37 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 346.1 seconds

RetCode: 0

Status:  OK

CheckDir: vulcan.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings vulcan_1.5.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/vulcan.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* using platform: x86_64-pc-linux-gnu (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 ‘1.5.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
average_fragment_length 6.274  0.172   6.679
* 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/vulcan.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL vulcan
###
##############################################################################
##############################################################################


* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘vulcan’ ...
** using staged installation
** 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 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 (vulcan)

name	user	system	elapsed
average_fragment_length	6.274	0.172	6.679
corr2p	0.002	0.000	0.002
densityauc	0.038	0.000	0.038
dpareto	0.001	0.004	0.005
fisherp	0.000	0.000	0.001
gsea	1.219	0.004	1.223
kmgformat	0.009	0.003	0.012
null_gsea	0.023	0.000	0.023
p2corr	0.000	0.000	0.001
p2z	0	0	0
pareto.fit	0.006	0.000	0.007
plot_gsea	0.03	0.00	0.03
ppareto	0.004	0.000	0.003
rea	0.003	0.000	0.002
slice	0	0	0
stouffer	0.001	0.000	0.000
textplot2	0.176	0.020	0.196
val2col	0.001	0.004	0.005
vulcan	3.356	0.028	3.523
vulcan.annotate	1.658	0.048	1.705
vulcan.import	0.020	0.000	0.019
vulcan.normalize	0	0	0
vulcan.pathways	2.196	0.000	2.196
wstouffer	0.000	0.000	0.001
z2p	0	0	0