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CHECK report for chroGPS on malbec2

This page was generated on 2018-10-17 08:24:41 -0400 (Wed, 17 Oct 2018).

Package 240/1561HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.28.0
Oscar Reina
Snapshot Date: 2018-10-15 16:45:08 -0400 (Mon, 15 Oct 2018)
URL: https://git.bioconductor.org/packages/chroGPS
Branch: RELEASE_3_7
Last Commit: 5543f26
Last Changed Date: 2018-04-30 10:35:27 -0400 (Mon, 30 Apr 2018)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
merida2 OS X 10.11.6 El Capitan / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 1.28.0
Command: /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings chroGPS_1.28.0.tar.gz
StartedAt: 2018-10-15 23:13:41 -0400 (Mon, 15 Oct 2018)
EndedAt: 2018-10-15 23:15:13 -0400 (Mon, 15 Oct 2018)
EllapsedTime: 92.4 seconds
RetCode: 0
Status:  OK 
CheckDir: chroGPS.Rcheck
Warnings: 0

Command output

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### Running command:
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###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD check --install=check:chroGPS.install-out.txt --library=/home/biocbuild/bbs-3.7-bioc/R/library --no-vignettes --timings chroGPS_1.28.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.7-bioc/meat/chroGPS.Rcheck’
* using R version 3.5.1 Patched (2018-07-12 r74967)
* 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 ‘1.28.0’
* 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 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
  ‘/home/biocbuild/bbs-3.7-bioc/meat/chroGPS.Rcheck/00check.log’
for details.



Installation output

chroGPS.Rcheck/00install.out

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### Running command:
###
###   /home/biocbuild/bbs-3.7-bioc/R/bin/R CMD INSTALL chroGPS
###
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* installing to library ‘/home/biocbuild/bbs-3.7-bioc/R/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)

Tests output


Example timings

chroGPS.Rcheck/chroGPS-Ex.timings

nameusersystemelapsed
addVar0.0000.0000.001
adjustPeaks000
boostMDS0.0000.0000.001
clusGPS-class0.0040.0000.001
clusGPS0.0000.0000.001
distGPS-class0.0040.0000.002
distGPS0.0680.0000.069
domainDist0.0000.0000.001
geneSetGPS0.0000.0000.001
getURL000
gff2RDList000
gps2xgmml0.0000.0000.001
mds-class0.0000.0000.001
mds0.1040.0000.103
mergeClusters000
procrustesAdj1.3920.0321.425
profileClusters0.0000.0000.001
s20.2160.0000.216
splitDistGPS-class0.0000.0000.001