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BioC 3.1: CHECK report for phenoTest on moscato2

This page was generated on 2015-10-09 09:29:05 -0700 (Fri, 09 Oct 2015).

Package 715/1024HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
phenoTest 1.16.0
Evarist Planet
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/phenoTest
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  OK  OK  OK UNNEEDED, same version exists in internal repository
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK [ OK ] OK UNNEEDED, same version exists in internal repository
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: phenoTest
Version: 1.16.0
Command: rm -rf phenoTest.buildbin-libdir phenoTest.Rcheck && mkdir phenoTest.buildbin-libdir phenoTest.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.16.0.tar.gz >phenoTest.Rcheck\00install.out 2>&1 && cp phenoTest.Rcheck\00install.out phenoTest-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.16.0.tar.gz
StartedAt: 2015-10-09 04:47:25 -0700 (Fri, 09 Oct 2015)
EndedAt: 2015-10-09 04:54:22 -0700 (Fri, 09 Oct 2015)
EllapsedTime: 416.6 seconds
RetCode: 0
Status:  OK  
CheckDir: phenoTest.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   rm -rf phenoTest.buildbin-libdir phenoTest.Rcheck && mkdir phenoTest.buildbin-libdir phenoTest.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.16.0.tar.gz >phenoTest.Rcheck\00install.out 2>&1 && cp phenoTest.Rcheck\00install.out phenoTest-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/phenoTest.Rcheck'
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'phenoTest/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'phenoTest' version '1.16.0'
* 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 'phenoTest' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Title field: should not end in a period.
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
* 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
* 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 dependencies in R code ... NOTE
'library' or 'require' call to 'ggplot2' which was already attached by Depends.
  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' '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
ClusterPhenoTest: no visible global function definition for 'pData'
ClusterPhenoTest : <anonymous>: no visible global function definition
  for 'pData'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'pData'
ExpressionPhenoTest : mycoxph: no visible global function definition
  for 'bic.surv'
ExpressionPhenoTest: no visible global function definition for 'exprs'
ExpressionPhenoTest: no visible global function definition for 'pData'
ExpressionPhenoTest : <anonymous>: no visible global function
  definition for 'pData'
ExpressionPhenoTest: no visible binding for global variable 'y'
ExpressionPhenoTest: no visible global function definition for
  'featureNames'
ExpressionPhenoTest: no visible global function definition for
  'annotation'
epheno2html: no visible global function definition for 'annotation'
epheno2html: no visible global function definition for 'featureNames'
epheno2html : export2html: no visible global function definition for
  'featureNames'
epheno2html : export2html: no visible global function definition for
  'annotation'
epheno2html : export2html: no visible global function definition for
  'pData'
epheno2html : export2html: no visible global function definition for
  'exprs'
epheno2html : export2html : myFun: no visible global function
  definition for 'featureNames'
epheno2html : export2html : myFun: no visible global function
  definition for 'pData'
epheno2html : export2html : myFun: no visible global function
  definition for 'exprs'
eset2genelevel: no visible global function definition for 'annotation'
eset2genelevel: no visible global function definition for
  'featureNames<-'
eset2genelevel: no visible global function definition for
  'annotation<-'
getEsPositions: no visible global function definition for 'annotation'
getEsPositions: no visible global function definition for
  'featureNames'
gsea.go: no visible global function definition for 'featureNames'
gsea.kegg: no visible global function definition for 'featureNames'
gsea2html: no visible global function definition for 'annotation'
gsea2html: no visible global function definition for 'exprs'
gsea2html: no visible global function definition for 'pData'
gsea2html: no visible global function definition for 'featureNames'
gsea2html: no visible global function definition for 'Term'
pca: no visible global function definition for 'exprs'
pca.2d: no visible global function definition for 'pData'
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'
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
  for 'featureNames'
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
  for 'exprs<-'
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
  for 'exprs'
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
  for 'pData'
[,epheno-ANY-ANY-ANY : .local: no visible global function definition
  for 'pData<-'
barplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'featureNames'
barplotSignatures,epheno-list : <anonymous> : <anonymous>: no visible
  global function definition for 'featureNames'
barplotSignifSignatures,epheno-list : <anonymous>: no visible global
  function definition for 'featureNames'
barplotSignifSignatures,epheno-list : myFun1 : <anonymous>: no visible
  global function definition for 'featureNames'
boxplotSignatures,epheno-list : <anonymous>: no visible global function
  definition for 'featureNames'
dim,epheno: no visible global function definition for 'exprs'
dim,epheno: no visible global function definition for 'pData'
export2CSV,epheno: no visible global function definition for 'fData'
export2CSV,epheno: no visible global function definition for
  'featureNames'
getFc,epheno: no visible global function definition for 'pData'
getFc,epheno: no visible global function definition for 'exprs'
getHr,epheno: no visible global function definition for 'pData'
getHr,epheno: no visible global function definition for 'exprs'
getMeans,epheno: no visible global function definition for 'pData'
getMeans,epheno: no visible global function definition for 'exprs'
getPostProbs,epheno: no visible global function definition for 'pData'
getPostProbs,epheno: no visible global function definition for 'exprs'
getPvals,epheno: no visible global function definition for 'pData'
getPvals,epheno: no visible global function definition for 'exprs'
getSignif,epheno: no visible global function definition for 'pData'
getSignif,epheno: no visible global function definition for 'exprs'
getSummaryDif,epheno: no visible global function definition for 'pData'
getSummaryDif,epheno: no visible global function definition for 'exprs'
getVars2test,epheno: no visible global function definition for 'pData'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'pData'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'featureNames'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'annotation'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'exprs<-'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'exprs'
heatmapPhenoTest,ExpressionSet-character: no visible global function
  definition for 'heatmap_plus'
heatmapPhenoTest,ExpressionSet-missing: no visible global function
  definition for 'featureNames'
pAdjust,epheno: no visible global function definition for 'pData'
pAdjust,epheno: no visible global function definition for 'exprs'
pAdjust,epheno: no visible global function definition for 'exprs<-'
phenoClass,epheno: no visible global function definition for 'pData'
phenoNames,epheno: no visible global function definition for 'pData'
show,epheno: no visible global function definition for 'featureNames'
show,epheno: no visible global function definition for 'annotation'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [27s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExpressionPhenoTest 6.80   0.07    6.87
findCopyNumber      6.19   0.00    6.19
** running examples for arch 'x64' ... [31s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExpressionPhenoTest 8.98   0.00    8.99
findCopyNumber      5.79   0.03    5.82
* 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: 4 NOTEs
See
  'E:/biocbld/bbs-3.1-bioc/meat/phenoTest.Rcheck/00check.log'
for details.


phenoTest.Rcheck/00install.out:


install for i386

* installing *source* package 'phenoTest' ...
** 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 'GSEABase::union' when loading 'HTSanalyzeR'
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
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
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?)

install for x64

* installing *source* package 'phenoTest' ...
** testing if installed package can be loaded
Creating a generic function for 'nchar' from package 'base' in package 'S4Vectors'
Warning: replacing previous import by 'GSEABase::union' when loading 'HTSanalyzeR'
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?)
* MD5 sums
packaged installation of 'phenoTest' as phenoTest_1.16.0.zip
* DONE (phenoTest)

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

nameusersystemelapsed
ClusterPhenoTest0.180.000.19
ExpressionPhenoTest6.800.076.87
epheno-class000
epheno0.020.020.04
epheno2html000
eset0.140.020.15
eset.genelevel0.090.000.10
eset2genelevel000
findCopyNumber6.190.006.19
genesInArea0.190.000.28
getEsPositions0.160.010.17
getGo000
getKegg000
getVars2test0.030.000.03
gsea0.290.020.31
gsea.kegg.go000
gsea2html0.610.010.62
gseaData-class000
gseaSignatures-class000
gseaSignatures0.040.000.03
gseaSignaturesSign-class000
gseaSignaturesVar-class000
gseaSignificance000
gseaSignificanceSign-class000
gseaSignificanceVar-class000
heatmapPhenoTest0.300.020.31
pAdjust0.030.000.03
pca0.480.030.51
plot.gsea000
plot.gseaSignatures000
plots4epheno0.050.000.05
smoothCoxph0.160.000.15
summary.gsea000
summary.gseaSignificance000
write.html000

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

nameusersystemelapsed
ClusterPhenoTest0.190.020.20
ExpressionPhenoTest8.980.008.99
epheno-class000
epheno0.020.020.03
epheno2html000
eset0.120.000.12
eset.genelevel0.10.00.1
eset2genelevel0.010.000.01
findCopyNumber5.790.035.82
genesInArea0.180.000.17
getEsPositions0.150.010.17
getGo000
getKegg000
getVars2test0.030.000.03
gsea0.330.000.33
gsea.kegg.go000
gsea2html0.720.050.76
gseaData-class000
gseaSignatures-class000
gseaSignatures0.030.000.03
gseaSignaturesSign-class000
gseaSignaturesVar-class000
gseaSignificance000
gseaSignificanceSign-class000
gseaSignificanceVar-class000
heatmapPhenoTest0.320.040.36
pAdjust0.030.000.03
pca0.500.010.52
plot.gsea000
plot.gseaSignatures000
plots4epheno0.070.000.06
smoothCoxph0.150.000.16
summary.gsea000
summary.gseaSignificance000
write.html000