Package: vulcan

Version: 1.0.0

Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings vulcan_1.0.0.tar.gz

StartedAt: 2018-04-12 03:34:46 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 03:39:58 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 312.2 seconds

RetCode: 0

Status:  OK

CheckDir: vulcan.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings vulcan_1.0.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/vulcan.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.0.0’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                        user system elapsed
average_fragment_length 8.36  0.136   8.824
* 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-3.6-bioc/meat/vulcan.Rcheck/00check.log’
for details.

* installing *source* package ‘vulcan’ ...
** R
** inst
** preparing 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	8.360	0.136	8.824
corr2p	0.000	0.000	0.002
densityauc	0.072	0.000	0.072
dpareto	0.004	0.000	0.004
fisherp	0.004	0.000	0.001
gsea	0.180	0.020	0.199
kmgformat	0.032	0.000	0.034
null_gsea	0.036	0.000	0.038
p2corr	0.004	0.000	0.000
p2z	0	0	0
pareto.fit	0.016	0.004	0.018
plot_gsea	0.072	0.000	0.071
ppareto	0.004	0.000	0.005
rea	0.004	0.000	0.003
slice	0.004	0.000	0.001
stouffer	0	0	0
textplot2	0.272	0.000	0.270
val2col	0.052	0.000	0.051
vulcan	4.616	0.020	4.639
vulcan.annotate	1.568	0.008	1.575
vulcan.import	0.044	0.000	0.046
vulcan.normalize	0.000	0.000	0.001
vulcan.pathways	1.748	0.000	1.749
wstouffer	0	0	0
z2p	0.000	0.000	0.001