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BioC 3.0: CHECK report for chroGPS on moscato1

This page was generated on 2015-04-10 09:48:17 -0700 (Fri, 10 Apr 2015).

Package 155/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.10.0
Oscar Reina
Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/chroGPS
Last Changed Rev: 95439 / Revision: 102249
Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014)
zin1 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  WARNINGS 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK [ WARNINGS ] OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  WARNINGS  OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK 

Summary

Package: chroGPS
Version: 1.10.0
Command: rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.10.0.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.10.0.tar.gz
StartedAt: 2015-04-09 23:44:01 -0700 (Thu, 09 Apr 2015)
EndedAt: 2015-04-09 23:47:16 -0700 (Thu, 09 Apr 2015)
EllapsedTime: 194.6 seconds
RetCode: 0
Status:  WARNINGS  
CheckDir: chroGPS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf chroGPS.buildbin-libdir chroGPS.Rcheck && mkdir chroGPS.buildbin-libdir chroGPS.Rcheck && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=chroGPS.buildbin-libdir chroGPS_1.10.0.tar.gz >chroGPS.Rcheck\00install.out 2>&1 && cp chroGPS.Rcheck\00install.out chroGPS-install.out  && D:\biocbld\bbs-3.0-bioc\R\bin\R.exe CMD check --library=chroGPS.buildbin-libdir --install="check:chroGPS-install.out" --force-multiarch --no-vignettes --timings chroGPS_1.10.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'D:/biocbld/bbs-3.0-bioc/meat/chroGPS.Rcheck'
* using R version 3.1.3 (2015-03-09)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'chroGPS/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'chroGPS' version '1.10.0'
* 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 whether package 'chroGPS' can be installed ... WARNING
Found the following significant warnings:
  Warning: replacing previous import by 'graphics::plot' when loading 'chroGPS'
See 'D:/biocbld/bbs-3.0-bioc/meat/chroGPS.Rcheck/00install.out' for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  'graphics'
A package should be listed in only one of these fields.
* 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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
Packages in Depends field not imported from:
  'Biobase' 'MASS' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' calls which should be '::':
  'changepoint:::cpt.var' 'changepoint:::plot'
  See the note in ?`:::` about the use of this operator.
Missing object imported by a ':::' call: '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
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'
gps2xgmml: no visible global function definition for 'col2hex'
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'
mds,distGPS-missing: no visible global function definition for 'isoMDS'
* 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 ...
** running examples for arch 'i386' ... [8s] OK
** running examples for arch 'x64' ... [11s] OK
* 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

WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
  'D:/biocbld/bbs-3.0-bioc/meat/chroGPS.Rcheck/00check.log'
for details.

chroGPS.Rcheck/00install.out:


install for i386

* installing *source* package 'chroGPS' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by 'graphics::plot' when loading 'chroGPS'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::plot' when loading 'chroGPS'

install for x64

* installing *source* package 'chroGPS' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::plot' when loading 'chroGPS'
* MD5 sums
packaged installation of 'chroGPS' as chroGPS_1.10.0.zip
* DONE (chroGPS)

chroGPS.Rcheck/examples_i386/chroGPS-Ex.timings:

nameusersystemelapsed
addVar000
adjustPeaks000
boostMDS000
clusGPS-class000
clusGPS000
distGPS-class000
distGPS0.050.000.05
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml000
mds-class000
mds0.010.000.05
mergeClusters000
procrustesAdj2.220.162.96
profileClusters000
s20.550.030.58
splitDistGPS-class000

chroGPS.Rcheck/examples_x64/chroGPS-Ex.timings:

nameusersystemelapsed
addVar000
adjustPeaks000
boostMDS000
clusGPS-class000
clusGPS000
distGPS-class000
distGPS0.030.000.03
domainDist000
geneSetGPS000
getURL000
gff2RDList000
gps2xgmml000
mds-class0.010.000.01
mds000
mergeClusters000
procrustesAdj2.640.113.57
profileClusters000
s20.530.010.54
splitDistGPS-class000