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

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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_2.2.0.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.

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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	0.000	0.001
adjustPeaks	0.001	0.000	0.000
bg3	0.253	0.013	0.266
boostMDS	0	0	0
clusGPS-class	0.001	0.000	0.002
clusGPS	0.000	0.000	0.001
combineGenesMatrix	0.000	0.000	0.001
diffFactors	0.311	0.030	0.343
diffGenes	0.001	0.002	0.003
distGPS-class	0.094	0.011	0.105
distGPS	0.024	0.003	0.026
domainDist	0.001	0.000	0.001
geneSetGPS	0.000	0.001	0.001
getURL	0.000	0.001	0.000
gff2RDList	0.001	0.000	0.000
gps2xgmml	0.000	0.001	0.000
mds-class	0.000	0.000	0.001
mds	0.042	0.002	0.045
mergeClusters	0.001	0.000	0.001
mergeReplicates	0.001	0.001	0.001
procrustesAdj	6.931	0.576	7.509
profileClusters	0.000	0.001	0.000
rankFactorsbyDomain	0.102	0.008	0.109
rankFactorsbyProfile	119.233	24.076	145.353
s2	0.237	0.027	0.264
splitDistGPS-class	0.001	0.001	0.001