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CHECK report for chroGPS on malbec1

This page was generated on 2018-04-12 13:10:43 -0400 (Thu, 12 Apr 2018).

Package 227/1472HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.27.3
Oscar Reina
Snapshot Date: 2018-04-11 16:45:18 -0400 (Wed, 11 Apr 2018)
URL: https://git.bioconductor.org/packages/chroGPS
Branch: RELEASE_3_6
Last Commit: 65f25f8
Last Changed Date: 2018-04-10 14:53:54 -0400 (Tue, 10 Apr 2018)
malbec1 Linux (Ubuntu 16.04.1 LTS) / x86_64  NotNeeded  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay1 Windows Server 2012 R2 Standard / x64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository
veracruz1 OS X 10.11.6 El Capitan / x86_64  NotNeeded  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 1.27.3
Command: /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chroGPS_1.27.3.tar.gz
StartedAt: 2018-04-11 22:15:14 -0400 (Wed, 11 Apr 2018)
EndedAt: 2018-04-11 22:17:09 -0400 (Wed, 11 Apr 2018)
EllapsedTime: 114.5 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

##############################################################################
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### Running command:
###
###   /home/biocbuild/bbs-3.6-bioc/R/bin/R CMD check --no-vignettes --timings chroGPS_1.27.3.tar.gz
###
##############################################################################
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* using log directory ‘/home/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck’
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-pc-linux-gnu (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 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 6.08  0.076    6.16
* 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
  ‘/home/biocbuild/bbs-3.6-bioc/meat/chroGPS.Rcheck/00check.log’
for details.



Installation output

chroGPS.Rcheck/00install.out

* 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)

Tests output


Example timings

chroGPS.Rcheck/chroGPS-Ex.timings

nameusersystemelapsed
addVar0.0040.0000.000
adjustPeaks000
boostMDS000
clusGPS-class0.0000.0000.001
clusGPS0.0000.0000.001
distGPS-class0.0000.0000.001
distGPS0.2160.0000.216
domainDist0.0040.0000.000
geneSetGPS0.0000.0000.001
getURL0.0000.0000.001
gff2RDList0.0000.0000.001
gps2xgmml000
mds-class000
mds0.0320.0000.032
mergeClusters0.0000.0000.001
procrustesAdj6.0800.0766.160
profileClusters0.0040.0000.001
s20.1920.0000.191
splitDistGPS-class000