Package: chroGPS

Version: 1.28.0

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_1.28.0.tar.gz

StartedAt: 2018-10-16 20:26:45 -0400 (Tue, 16 Oct 2018)

EndedAt: 2018-10-16 20:29:03 -0400 (Tue, 16 Oct 2018)

EllapsedTime: 137.1 seconds

RetCode: 0

Status:  OK

CheckDir: chroGPS.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### 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_1.28.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.7-bioc/meat/chroGPS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 ... NOTE
Missing or unexported object: ‘changepoint::cpt.method’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
avgdistpair: no visible global function definition for ‘%over%’
chisqdist : <anonymous>: no visible global function definition for
  ‘RleList’
chisqdist : <anonymous> : <anonymous>: no visible global function
  definition for ‘Rle’
chisqdist2: no visible global function definition for ‘mclapply’
contour2dDP: no visible binding for global variable ‘state’
gff2RDList: no visible global function definition for ‘GenomicRanges’
gps2xgmml: no visible global function definition for ‘col2hex’
realtanipair: no visible global function definition for ‘%over%’
uniqueCount: no visible binding for global variable ‘u’
xgmml2d: no visible global function definition for ‘xmlOutputDOM’
xgmml2d: no visible global function definition for ‘saveXML’
xgmml3d: no visible global function definition for ‘xmlOutputDOM’
xgmml3d: no visible global function definition for ‘saveXML’
gps2xgmml,mds: no visible global function definition for ‘col2hex’
plot,mds-ANY: no visible global function definition for ‘plot3d’
plot,mds-ANY: no visible global function definition for ‘text3d’
plot,mds-ANY: no visible global function definition for ‘spheres3d’
Undefined global functions or variables:
  %over% GenomicRanges Rle RleList col2hex mclapply plot3d saveXML
  spheres3d state text3d u xmlOutputDOM
* 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 files in ‘vignettes’ ... OK
* checking examples ... OK
* checking for unstated dependencies in vignettes ... OK
* 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-3.7-bioc/meat/chroGPS.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL chroGPS
###
##############################################################################
##############################################################################


* 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
** testing if installed package can be loaded
* DONE (chroGPS)

name	user	system	elapsed
addVar	0.001	0.000	0.001
adjustPeaks	0.001	0.000	0.000
boostMDS	0.002	0.000	0.002
clusGPS-class	0.001	0.000	0.002
clusGPS	0.002	0.000	0.002
distGPS-class	0.002	0.001	0.003
distGPS	0.096	0.004	0.105
domainDist	0.001	0.000	0.001
geneSetGPS	0.001	0.000	0.001
getURL	0.000	0.000	0.001
gff2RDList	0.001	0.000	0.001
gps2xgmml	0.001	0.001	0.002
mds-class	0.003	0.000	0.002
mds	0.011	0.001	0.012
mergeClusters	0.001	0.000	0.002
procrustesAdj	2.056	0.073	2.159
profileClusters	0.002	0.000	0.001
s2	0.278	0.023	0.306
splitDistGPS-class	0.001	0.000	0.001