Package: chroGPS

Version: 2.0.1

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_2.0.1.tar.gz

StartedAt: 2019-04-15 22:57:47 -0400 (Mon, 15 Apr 2019)

EndedAt: 2019-04-15 23:02:21 -0400 (Mon, 15 Apr 2019)

EllapsedTime: 273.9 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_2.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/chroGPS.Rcheck’
* using R version 3.5.3 (2019-03-11)
* 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 ‘2.0.1’
* 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 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 113.155 11.927 126.979
* 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-3.8-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/3.5/Resources/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)

name	user	system	elapsed
addVar	0.000	0.001	0.001
adjustPeaks	0.001	0.000	0.000
bg3	0.319	0.008	0.329
boostMDS	0	0	0
clusGPS-class	0.001	0.000	0.001
clusGPS	0	0	0
combineGenesMatrix	0.000	0.001	0.000
diffFactors	0.291	0.015	0.309
diffGenes	0.001	0.001	0.002
distGPS-class	0.119	0.006	0.126
distGPS	0.022	0.002	0.023
domainDist	0.000	0.000	0.001
geneSetGPS	0.000	0.001	0.000
getURL	0.000	0.000	0.001
gff2RDList	0.000	0.000	0.001
gps2xgmml	0	0	0
mds-class	0.001	0.000	0.001
mds	0.009	0.001	0.009
mergeClusters	0.000	0.000	0.001
mergeReplicates	0.000	0.001	0.001
procrustesAdj	4.681	0.246	4.963
profileClusters	0.001	0.000	0.000
rankFactorsbyDomain	0.100	0.005	0.106
rankFactorsbyProfile	113.155	11.927	126.979
s2	0.226	0.016	0.251
splitDistGPS-class	0.001	0.000	0.001