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CHECK report for vulcan on malbec1

This page was generated on 2019-04-16 11:53:04 -0400 (Tue, 16 Apr 2019).

Package 1627/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
vulcan 1.4.0
Federico M. Giorgi
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/vulcan
Branch: RELEASE_3_8
Last Commit: 5848876
Last Changed Date: 2018-10-30 11:42:06 -0400 (Tue, 30 Oct 2018)
malbec1 Linux (Ubuntu 16.04.6 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
merida1 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: vulcan
Version: 1.4.0
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings vulcan_1.4.0.tar.gz
StartedAt: 2019-04-16 03:39:49 -0400 (Tue, 16 Apr 2019)
EndedAt: 2019-04-16 03:45:33 -0400 (Tue, 16 Apr 2019)
EllapsedTime: 343.8 seconds
RetCode: 0
Status:  OK 
CheckDir: vulcan.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:vulcan.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings vulcan_1.4.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/vulcan.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘1.4.0’
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
                         user system elapsed
average_fragment_length 7.704  0.192   8.691
* 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-3.8-bioc/meat/vulcan.Rcheck/00check.log’
for details.



Installation output

vulcan.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL vulcan
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/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)

Tests output


Example timings

vulcan.Rcheck/vulcan-Ex.timings

nameusersystemelapsed
average_fragment_length7.7040.1928.691
corr2p0.0040.0000.002
densityauc0.0200.0040.027
dpareto0.0000.0000.003
fisherp000
gsea1.1000.0201.122
kmgformat0.0120.0000.012
null_gsea0.0240.0000.022
p2corr000
p2z0.0040.0000.000
pareto.fit0.0040.0000.007
plot_gsea0.0240.0040.028
ppareto0.0040.0000.004
rea0.0000.0040.002
slice000
stouffer000
textplot20.1960.0280.225
val2col0.0040.0000.005
vulcan2.7160.0322.770
vulcan.annotate1.4120.0121.427
vulcan.import0.0280.0040.031
vulcan.normalize0.0000.0000.001
vulcan.pathways1.9920.0001.992
wstouffer000
z2p000