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BioC 3.0: CHECK report for phenoTest on perceval

This page was generated on 2015-04-10 09:55:34 -0700 (Fri, 10 Apr 2015).

Package 657/933HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.14.0
Evarist Planet
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/phenoTest
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  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  NotNeeded  OK  OK  OK 
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  NotNeeded  OK [ OK ] OK 
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  NotNeeded  OK  OK  OK 

Summary

Package: phenoTest
Version: 1.14.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch phenoTest_1.14.0.tar.gz
StartedAt: 2015-04-10 04:46:38 -0700 (Fri, 10 Apr 2015)
EndedAt: 2015-04-10 04:57:28 -0700 (Fri, 10 Apr 2015)
EllapsedTime: 650.3 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_1.14.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/phenoTest.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (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 ‘1.14.0’
* 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 ... [57s/61s] 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:
  ‘annotate’ ‘BMA’ ‘ggplot2’ ‘gridExtra’ ‘Heatplus’ ‘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’
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ExpressionPhenoTest : mycoxph: no visible global function definition
  for ‘bic.surv’
ExpressionPhenoTest: no visible binding for global variable ‘y’
pca.2d: no visible global function definition for ‘qplot’
pca.2d: no visible binding for global variable ‘pc1’
pca.2d: no visible binding for global variable ‘pc2’
pca.2d: no visible global function definition for ‘geom_point’
pca.2d: no visible global function definition for ‘coord_cartesian’
pca.2d: no visible global function definition for ‘theme’
pca.2d: no visible global function definition for ‘ggtitle’
pca.multipleDim: no visible global function definition for
  ‘grid.newpage’
pca.multipleDim: no visible global function definition for
  ‘pushViewport’
pca.multipleDim: no visible global function definition for ‘viewport’
pca.multipleDim: no visible global function definition for
  ‘grid.layout’
pca.multipleDim: no visible global function definition for ‘unit’
pca.multipleDim : vplayout: no visible global function definition for
  ‘viewport’
pca.multipleDim: no visible global function definition for ‘ggplot’
pca.multipleDim: no visible global function definition for ‘aes’
pca.multipleDim: no visible global function definition for ‘geom_text’
pca.multipleDim: no visible global function definition for ‘theme’
pca.multipleDim: no visible global function definition for
  ‘element_blank’
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’
pca.multipleDim: no visible global function definition for ‘geom_point’
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for ‘heatmap_plus’
* 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 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 ... [50s/50s] OK
Examples with CPU or elapsed time > 5s
                      user system elapsed
ExpressionPhenoTest 10.394  0.157  10.592
findCopyNumber       7.277  0.314   7.594
* 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

NOTE: There were 5 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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 in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "head" from package "AnnotationDbi" (malformed exports?)
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Warning in namespaceImportMethods(ns, loadNamespace(j <- imp[[1L]], c(lib.loc,  :
  No generic function found corresponding to requested imported methods for "head" from package "AnnotationDbi" (malformed exports?)
* DONE (phenoTest)

phenoTest.Rcheck/phenoTest-Ex.timings:

nameusersystemelapsed
ClusterPhenoTest0.2210.0120.234
ExpressionPhenoTest10.394 0.15710.592
epheno-class0.0020.0010.002
epheno0.0220.0010.024
epheno2html0.0010.0000.000
eset0.1170.0020.119
eset.genelevel0.0830.0020.084
eset2genelevel0.0000.0010.000
findCopyNumber7.2770.3147.594
genesInArea0.3240.0110.336
getEsPositions0.2880.0070.295
getGo0.0010.0000.001
getKegg0.0010.0000.001
getVars2test0.0260.0020.026
gsea0.3330.0120.346
gsea.kegg.go0.0010.0000.001
gsea2html0.7430.0280.771
gseaData-class0.0020.0000.002
gseaSignatures-class0.0020.0000.001
gseaSignatures0.0260.0020.028
gseaSignaturesSign-class0.0020.0000.003
gseaSignaturesVar-class0.0010.0000.001
gseaSignificance0.0010.0000.001
gseaSignificanceSign-class0.0010.0000.001
gseaSignificanceVar-class0.0010.0000.002
heatmapPhenoTest0.3670.0100.403
pAdjust0.0280.0010.030
pca1.9090.0281.958
plot.gsea0.0010.0000.000
plot.gseaSignatures0.0010.0000.000
plots4epheno0.0630.0050.076
smoothCoxph0.1590.0090.176
summary.gsea0.0000.0000.001
summary.gseaSignificance0.0000.0000.001
write.html0.0010.0000.001