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BioC 3.1: CHECK report for chroGPS on petty

This page was generated on 2015-10-09 09:35:20 -0700 (Fri, 09 Oct 2015).

Package 165/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
chroGPS 1.12.0
Oscar Reina
Snapshot Date: 2015-10-08 17:20:21 -0700 (Thu, 08 Oct 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_1/madman/Rpacks/chroGPS
Last Changed Rev: 102591 / Revision: 109384
Last Changed Date: 2015-04-16 12:42:01 -0700 (Thu, 16 Apr 2015)
zin2 Linux (Ubuntu 14.04.2 LTS) / x86_64  NotNeeded  OK  WARNINGS UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ WARNINGS ] OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  WARNINGS  OK UNNEEDED, same version exists in internal repository

Summary

Package: chroGPS
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chroGPS_1.12.0.tar.gz
StartedAt: 2015-10-08 22:02:44 -0700 (Thu, 08 Oct 2015)
EndedAt: 2015-10-08 22:05:15 -0700 (Thu, 08 Oct 2015)
EllapsedTime: 151.2 seconds
RetCode: 0
Status:  WARNINGS 
CheckDir: chroGPS.Rcheck
Warnings: 1

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings chroGPS_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/chroGPS.Rcheck’
* using R version 3.2.2 Patched (2015-08-14 r69078)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.12.0’
* 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 ... [12s/12s] WARNING
Found the following significant warnings:
  Warning: replacing previous import by ‘graphics::plot’ when loading ‘chroGPS’
See ‘/Users/biocbuild/bbs-3.1-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 ... 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
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’
plot,mds-ANY : .local: no visible global function definition for
  ‘plot3d’
plot,mds-ANY : .local: no visible global function definition for
  ‘text3d’
plot,mds-ANY : .local: no visible global function definition for
  ‘spheres3d’
* 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 ... [10s/13s] OK
Examples with CPU or elapsed time > 5s
               user system elapsed
procrustesAdj 2.739  0.219   6.269
* 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: 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/chroGPS.Rcheck/00check.log’
for details.


chroGPS.Rcheck/00install.out:

* installing *source* package ‘chroGPS’ ...
** R
** data
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
Warning: replacing previous import by ‘graphics::plot’ when loading ‘chroGPS’
* DONE (chroGPS)

chroGPS.Rcheck/chroGPS-Ex.timings:

nameusersystemelapsed
addVar000
adjustPeaks0.0000.0000.001
boostMDS0.0020.0000.002
clusGPS-class0.0020.0000.001
clusGPS0.0020.0000.002
distGPS-class0.0010.0000.002
distGPS0.0450.0020.047
domainDist0.0010.0000.002
geneSetGPS0.0020.0000.002
getURL0.0010.0000.000
gff2RDList0.0010.0000.001
gps2xgmml0.0010.0010.001
mds-class0.0010.0000.001
mds0.0180.0010.019
mergeClusters0.0010.0000.002
procrustesAdj2.7390.2196.269
profileClusters0.0010.0000.001
s20.8170.0190.837
splitDistGPS-class0.0010.0000.002