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CHECK report for chroGPS on malbec1

This page was generated on 2019-04-16 11:49:47 -0400 (Tue, 16 Apr 2019).

Package 255/1649HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 2.0.1
Oscar Reina
Snapshot Date: 2019-04-15 17:01:12 -0400 (Mon, 15 Apr 2019)
URL: https://git.bioconductor.org/packages/chroGPS
Branch: RELEASE_3_8
Last Commit: ac7ff10
Last Changed Date: 2018-12-10 05:59:15 -0400 (Mon, 10 Dec 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: chroGPS
Version: 2.0.1
Command: /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chroGPS_2.0.1.tar.gz
StartedAt: 2019-04-15 22:53:12 -0400 (Mon, 15 Apr 2019)
EndedAt: 2019-04-15 22:57:14 -0400 (Mon, 15 Apr 2019)
EllapsedTime: 241.9 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/home/biocbuild/bbs-3.8-bioc/R/library --no-vignettes --timings chroGPS_2.0.1.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.8-bioc/meat/chroGPS.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 ‘chroGPS/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘chroGPS’ version ‘2.0.1’
* 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 ‘chroGPS’ 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 ... NOTE
chisqdist : <anonymous>: no visible global function definition for
  ‘RleList’
chisqdist : <anonymous> : <anonymous>: no visible global function
  definition for ‘Rle’
Undefined global functions or variables:
  Rle RleList
* 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 contents of ‘data’ directory ... OK
* checking data for non-ASCII characters ... OK
* checking data for ASCII and uncompressed saves ... 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
rankFactorsbyProfile 105.488  0.072 105.879
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘gtools’
* 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: 2 NOTEs
See
  ‘/home/biocbuild/bbs-3.8-bioc/meat/chroGPS.Rcheck/00check.log’
for details.



Installation output

chroGPS.Rcheck/00install.out

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###
### Running command:
###
###   /home/biocbuild/bbs-3.8-bioc/R/bin/R CMD INSTALL chroGPS
###
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* installing to library ‘/home/biocbuild/bbs-3.8-bioc/R/library’
* installing *source* package ‘chroGPS’ ...
** R
** data
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   ‘chroGPS.Rnw’ 
** testing if installed package can be loaded
* DONE (chroGPS)

Tests output


Example timings

chroGPS.Rcheck/chroGPS-Ex.timings

nameusersystemelapsed
addVar0.0040.0000.000
adjustPeaks000
bg30.3480.0000.355
boostMDS000
clusGPS-class0.0040.0000.001
clusGPS000
combineGenesMatrix000
diffFactors0.3440.0080.353
diffGenes0.0000.0000.001
distGPS-class0.1160.0040.121
distGPS0.0120.0040.013
domainDist0.0000.0000.001
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml0.0040.0000.000
mds-class000
mds0.0040.0000.006
mergeClusters0.0000.0000.001
mergeReplicates000
procrustesAdj4.8360.0404.889
profileClusters000
rankFactorsbyDomain0.1200.0040.126
rankFactorsbyProfile105.488 0.072105.879
s20.2640.0040.267
splitDistGPS-class0.0000.0000.001