Package: chroGPS

Version: 2.4.0

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_2.4.0.tar.gz

StartedAt: 2019-12-18 01:25:54 -0500 (Wed, 18 Dec 2019)

EndedAt: 2019-12-18 01:30:54 -0500 (Wed, 18 Dec 2019)

EllapsedTime: 300.5 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

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### Running command:
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###   /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_2.4.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.10-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 ‘2.4.0’
* 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 112.507 11.422 126.617
procrustesAdj          9.266  0.360   9.963
* 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-3.10-bioc/meat/chroGPS.Rcheck/00check.log’
for details.

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### Running command:
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###   /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)

name	user	system	elapsed
addVar	0.000	0.001	0.000
adjustPeaks	0.000	0.000	0.001
bg3	0.399	0.009	0.415
boostMDS	0.000	0.000	0.001
clusGPS-class	0.001	0.000	0.002
clusGPS	0.000	0.000	0.001
combineGenesMatrix	0	0	0
diffFactors	0.390	0.019	0.420
diffGenes	0.000	0.001	0.002
distGPS-class	0.083	0.006	0.089
distGPS	0.022	0.001	0.023
domainDist	0	0	0
geneSetGPS	0.000	0.000	0.001
getURL	0.001	0.000	0.000
gff2RDList	0.000	0.000	0.001
gps2xgmml	0	0	0
mds-class	0.001	0.001	0.001
mds	0.01	0.00	0.01
mergeClusters	0	0	0
mergeReplicates	0.000	0.000	0.001
procrustesAdj	9.266	0.360	9.963
profileClusters	0	0	0
rankFactorsbyDomain	0.123	0.006	0.130
rankFactorsbyProfile	112.507	11.422	126.617
s2	0.257	0.012	0.270
splitDistGPS-class	0.001	0.000	0.001