Package: chroGPS

Version: 1.27.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chroGPS_1.27.3.tar.gz

StartedAt: 2018-04-12 01:41:08 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 01:43:24 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 136.5 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 --no-vignettes --timings chroGPS_1.27.3.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* 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 ‘1.27.3’
* 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 loading without being on the library search path ... 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 installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... OK
Examples with CPU or elapsed time > 5s
               user system elapsed
procrustesAdj 7.311   0.15   7.587
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' call not declared from: ‘gplots’
* 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck/00check.log’
for details.

* installing *source* package ‘chroGPS’ ...
** R
** data
** inst
** preparing 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	0.001	0.000	0.001
clusGPS-class	0.002	0.000	0.001
clusGPS	0.001	0.000	0.001
distGPS-class	0.001	0.001	0.001
distGPS	0.308	0.014	0.330
domainDist	0.001	0.000	0.001
geneSetGPS	0.001	0.001	0.001
getURL	0.001	0.000	0.001
gff2RDList	0.001	0.000	0.001
gps2xgmml	0.000	0.001	0.001
mds-class	0.001	0.000	0.001
mds	0.045	0.001	0.048
mergeClusters	0.001	0.000	0.001
procrustesAdj	7.311	0.150	7.587
profileClusters	0.001	0.000	0.000
s2	0.199	0.007	0.209
splitDistGPS-class	0.001	0.000	0.001