Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O [P] Q  R  S  T  U  V  W  X  Y  Z 

BioC 2.14: CHECK report for phenoTest on morelia

This page was generated on 2014-10-08 09:04:40 -0700 (Wed, 08 Oct 2014).

Package 580/824HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.12.0
Evarist Planet
Snapshot Date: 2014-10-07 17:20:37 -0700 (Tue, 07 Oct 2014)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_14/madman/Rpacks/phenoTest
Last Changed Rev: 88838 / Revision: 95116
Last Changed Date: 2014-04-11 14:07:21 -0700 (Fri, 11 Apr 2014)
zin2 Linux (Ubuntu 12.04.4 LTS) / x86_64  NotNeeded  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK  OK  OK 
morelia Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK [ OK ] OK 

Summary

Package: phenoTest
Version: 1.12.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.12.0.tar.gz
StartedAt: 2014-10-08 00:39:28 -0700 (Wed, 08 Oct 2014)
EndedAt: 2014-10-08 00:46:41 -0700 (Wed, 08 Oct 2014)
EllapsedTime: 433.5 seconds
RetCode: 0
Status:  OK 
CheckDir: phenoTest.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.12.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/phenoTest.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘phenoTest/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘phenoTest’ version ‘1.12.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘Biobase’ ‘annotate’ ‘Heatplus’ ‘BMA’ ‘ggplot2’ ‘gridExtra’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ‘phenoTest’ can be installed ... [38s/39s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘annotate’ ‘GSEABase’
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
* 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
'library' or 'require' calls to packages already attached by Depends:
  ‘ggplot2’ ‘gridExtra’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘annotate’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘BMA’ ‘Heatplus’ ‘annotate’ ‘ggplot2’ ‘gridExtra’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘sortDragHtmlTable’
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ExpressionPhenoTest: no visible binding for global variable ‘y’
pca.2d: no visible binding for global variable ‘pc1’
pca.2d: no visible binding for global variable ‘pc2’
pca.multipleDim: no visible binding for global variable ‘dummy1’
pca.multipleDim: no visible binding for global variable ‘dummy2’
pca.multipleDim: no visible binding for global variable ‘colour’
* 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 ... NOTE
S3 methods shown with full name in documentation object 'plot.gseaData':
  ‘plot.gseaData’

S3 methods shown with full name in documentation object 'plot.gseaSignatures':
  ‘plot.gseaSignaturesSign’

S3 methods shown with full name in documentation object 'summary.gseaData':
  ‘summary.gseaData’

S3 methods shown with full name in documentation object 'summary.gseaSignificance':
  ‘summary.gseaSignificanceSign’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See the chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 ... [34s/37s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ExpressionPhenoTest 6.977  0.064   7.050
findCopyNumber      5.352  0.197   5.733
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-2.14-bioc/meat/phenoTest.Rcheck/00check.log’
for details.

phenoTest.Rcheck/00install.out:

* installing *source* package ‘phenoTest’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning: replacing previous import by ‘graphics::image’ when loading ‘hopach’
* DONE (phenoTest)

phenoTest.Rcheck/phenoTest-Ex.timings:

nameusersystemelapsed
ClusterPhenoTest0.2290.0060.236
ExpressionPhenoTest6.9770.0647.050
epheno-class0.0030.0010.003
epheno0.0190.0000.020
epheno2html0.0010.0000.001
eset0.1490.0020.150
eset.genelevel0.1000.0010.102
eset2genelevel0.0000.0000.001
findCopyNumber5.3520.1975.733
genesInArea0.2440.0070.252
getEsPositions0.2290.0060.235
getGo0.0000.0000.001
getKegg0.0010.0000.000
getVars2test0.0240.0010.025
gsea0.2550.0160.271
gsea.kegg.go000
gsea2html0.7200.0120.733
gseaData-class0.0010.0000.002
gseaSignatures-class0.0010.0000.001
gseaSignatures0.0220.0010.028
gseaSignaturesSign-class0.0010.0000.001
gseaSignaturesVar-class0.0010.0000.001
gseaSignificance000
gseaSignificanceSign-class0.0020.0000.001
gseaSignificanceVar-class0.0020.0000.001
heatmapPhenoTest0.3800.0080.406
pAdjust0.0280.0010.029
pca1.9000.0171.919
plot.gsea000
plot.gseaSignatures0.0000.0000.001
plots4epheno0.0590.0020.079
smoothCoxph0.1680.0030.232
summary.gsea0.0010.0000.000
summary.gseaSignificance0.0010.0000.001
write.html0.0010.0000.001