BioC 2.13: CHECK report for phenoTest on moscato1

Package: phenoTest

Version: 1.10.0

Command: rm -rf phenoTest.buildbin-libdir && mkdir phenoTest.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=phenoTest.buildbin-libdir phenoTest_1.10.0.tar.gz >phenoTest-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=phenoTest.buildbin-libdir --install="check:phenoTest-install.out" --force-multiarch --no-vignettes --timings phenoTest_1.10.0.tar.gz && mv phenoTest.buildbin-libdir/* phenoTest.Rcheck/ && rmdir phenoTest.buildbin-libdir

StartedAt: 2014-04-05 05:49:32 -0700 (Sat, 05 Apr 2014)

EndedAt: 2014-04-05 05:59:25 -0700 (Sat, 05 Apr 2014)

EllapsedTime: 592.4 seconds

RetCode: 0

Status:  OK

CheckDir: phenoTest.Rcheck

Warnings: 0

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/phenoTest.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-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 '1.10.0'
* 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 'phenoTest' can be installed ... 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
* 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' 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
  'phenoTest.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [33s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
findCopyNumber      6.39   0.04    6.41
ExpressionPhenoTest 5.99   0.04    6.03
** running examples for arch 'x64' ... [40s] OK
Examples with CPU or elapsed time > 5s
                    user system elapsed
ExpressionPhenoTest 7.43   0.05    7.59
findCopyNumber      6.78   0.04    7.19
* 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
  'D:/biocbld/bbs-2.13-bioc/meat/phenoTest.Rcheck/00check.log'
for details.

install for i386

* 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'

install for x64

* installing *source* package 'phenoTest' ...
** testing if installed package can be loaded
Warning: replacing previous import by 'graphics::image' when loading 'hopach'
* MD5 sums
packaged installation of 'phenoTest' as phenoTest_1.10.0.zip
* DONE (phenoTest)

name	user	system	elapsed
ClusterPhenoTest	0.45	0.03	0.48
ExpressionPhenoTest	5.99	0.04	6.03
epheno-class	0	0	0
epheno	0.03	0.00	0.03
epheno2html	0	0	0
eset	0.12	0.02	0.14
eset.genelevel	0.08	0.01	0.09
eset2genelevel	0	0	0
findCopyNumber	6.39	0.04	6.41
genesInArea	0.33	0.00	0.46
getEsPositions	0.25	0.00	0.25
getGo	0.01	0.00	0.02
getKegg	0.02	0.00	0.01
getVars2test	0.03	0.00	0.04
gsea	0.29	0.00	0.30
gsea.kegg.go	0	0	0
gsea2html	0.72	0.01	0.73
gseaData-class	0.02	0.00	0.02
gseaSignatures-class	0.01	0.00	0.01
gseaSignatures	0.05	0.00	0.05
gseaSignaturesSign-class	0.01	0.00	0.02
gseaSignaturesVar-class	0	0	0
gseaSignificance	0	0	0
gseaSignificanceSign-class	0.02	0.00	0.02
gseaSignificanceVar-class	0	0	0
heatmapPhenoTest	0.34	0.00	0.34
pAdjust	0.03	0.02	0.05
pca	2.09	0.03	2.12
plot.gsea	0.02	0.00	0.01
plot.gseaSignatures	0	0	0
plots4epheno	0.06	0.00	0.06
smoothCoxph	0.16	0.00	0.15
summary.gsea	0	0	0
summary.gseaSignificance	0	0	0
write.html	0.02	0.00	0.02

name	user	system	elapsed
ClusterPhenoTest	0.23	0.02	0.25
ExpressionPhenoTest	7.43	0.05	7.59
epheno-class	0	0	0
epheno	0.03	0.00	0.03
epheno2html	0.00	0.01	0.01
eset	0.14	0.00	0.15
eset.genelevel	0.09	0.02	0.10
eset2genelevel	0	0	0
findCopyNumber	6.78	0.04	7.19
genesInArea	0.24	0.00	0.24
getEsPositions	0.20	0.02	0.21
getGo	0	0	0
getKegg	0.01	0.00	0.02
getVars2test	0.03	0.01	0.04
gsea	0.33	0.00	0.33
gsea.kegg.go	0.02	0.00	0.02
gsea2html	0.68	0.04	0.71
gseaData-class	0	0	0
gseaSignatures-class	0	0	0
gseaSignatures	0.04	0.00	0.03
gseaSignaturesSign-class	0	0	0
gseaSignaturesVar-class	0.02	0.00	0.01
gseaSignificance	0	0	0
gseaSignificanceSign-class	0	0	0
gseaSignificanceVar-class	0.02	0.00	0.01
heatmapPhenoTest	0.37	0.00	0.38
pAdjust	0.03	0.02	0.04
pca	2.52	0.03	2.55
plot.gsea	0	0	0
plot.gseaSignatures	0	0	0
plots4epheno	0.07	0.01	0.09
smoothCoxph	0.15	0.04	0.17
summary.gsea	0	0	0
summary.gseaSignificance	0.02	0.00	0.01
write.html	0.01	0.00	0.02