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CHECK report for chroGPS on celaya2

This page was generated on 2019-10-16 12:50:43 -0400 (Wed, 16 Oct 2019).

Package 269/1741HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 2.2.0
Oscar Reina
Snapshot Date: 2019-10-15 17:01:26 -0400 (Tue, 15 Oct 2019)
URL: https://git.bioconductor.org/packages/chroGPS
Branch: RELEASE_3_9
Last Commit: 77aa427
Last Changed Date: 2019-05-02 11:53:39 -0400 (Thu, 02 May 2019)
malbec2 Linux (Ubuntu 18.04.2 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
celaya2 OS X 10.11.6 El Capitan / x86_64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chroGPS_2.2.0.tar.gz
StartedAt: 2019-10-16 01:25:44 -0400 (Wed, 16 Oct 2019)
EndedAt: 2019-10-16 01:31:34 -0400 (Wed, 16 Oct 2019)
EllapsedTime: 350.2 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings chroGPS_2.2.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/chroGPS.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.2.0’
* 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 : : no visible global function definition for
  ‘RleList’
chisqdist :  : : 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 sizes of PDF files under ‘inst/doc’ ... 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 119.233 24.076 145.353
procrustesAdj          6.931  0.576   7.509
* 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
  ‘/Users/biocbuild/bbs-3.9-bioc/meat/chroGPS.Rcheck/00check.log’
for details.



Installation output

chroGPS.Rcheck/00install.out

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###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chroGPS
###
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘chroGPS’ ...
** using staged installation
** 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 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 (chroGPS)

Tests output


Example timings

chroGPS.Rcheck/chroGPS-Ex.timings

nameusersystemelapsed
addVar0.0000.0000.001
adjustPeaks0.0010.0000.000
bg30.2530.0130.266
boostMDS000
clusGPS-class0.0010.0000.002
clusGPS0.0000.0000.001
combineGenesMatrix0.0000.0000.001
diffFactors0.3110.0300.343
diffGenes0.0010.0020.003
distGPS-class0.0940.0110.105
distGPS0.0240.0030.026
domainDist0.0010.0000.001
geneSetGPS0.0000.0010.001
getURL0.0000.0010.000
gff2RDList0.0010.0000.000
gps2xgmml0.0000.0010.000
mds-class0.0000.0000.001
mds0.0420.0020.045
mergeClusters0.0010.0000.001
mergeReplicates0.0010.0010.001
procrustesAdj6.9310.5767.509
profileClusters0.0000.0010.000
rankFactorsbyDomain0.1020.0080.109
rankFactorsbyProfile119.233 24.076145.353
s20.2370.0270.264
splitDistGPS-class0.0010.0010.001