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Package 267/553HostnameOS / ArchBUILDCHECKBUILD BIN
HTSanalyzeR 2.8.3
Xin Wang
Snapshot Date: 2012-09-23 17:01:39 -0700 (Sun, 23 Sep 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_10/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 68710 / Revision: 69725
Last Changed Date: 2012-08-22 04:35:19 -0700 (Wed, 22 Aug 2012)
lamb2 Linux (openSUSE 11.4) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: HTSanalyzeR
Version: 2.8.3
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch HTSanalyzeR_2.8.3.tar.gz
StartedAt: 2012-09-24 00:34:45 -0700 (Mon, 24 Sep 2012)
EndedAt: 2012-09-24 00:39:42 -0700 (Mon, 24 Sep 2012)
EllapsedTime: 296.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.10-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 2.15.1 (2012-06-22)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.8.3'
* 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 whether package 'HTSanalyzeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
GOGeneSets: no visible binding for global variable 'org.Rn.egGo2EG'
* 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 examples ... OK
* 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There was 1 note.
See
  '/Users/biocbuild/bbs-2.10-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.

HTSanalyzeR.Rcheck/00install.out:

* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'
** help
*** installing help indices
** building package indices
** installing vignettes
   'HTSanalyzeR-Vignette.Rnw' 
** testing if installed package can be loaded
Warning: replacing previous import 'coerce' when loading 'cellHTS2'
Warning: replacing previous import 'initialize' when loading 'cellHTS2'

* DONE (HTSanalyzeR)

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings:

nameusersystemelapsed
FDRcollectionGsea0.7130.0380.751
GOGeneSets3.8950.2924.317
GSCA-class0.0000.0000.001
HTSanalyzeR4cellHTS20.0000.0000.001
KeggGeneSets3.6620.1113.792
NWA-class000
aggregatePvals0.0050.0000.006
analyze000
analyzeGeneSetCollections0.0000.0000.001
annotationConvertor1.2170.0411.290
appendGSTerms0.0010.0000.000
biogridDataDownload0.0000.0010.001
celAnnotationConvertor1.2020.0551.259
cellHTS2OutputStatTests0.0010.0000.000
collectionGsea0.3790.0290.409
data-KcViab1.4330.0371.470
drosoAnnotationConvertor0.8960.0220.918
duplicateRemover0.0010.0000.001
getTopGeneSets0.0010.0000.000
gseaPlots0.0000.0010.000
gseaScores0.0230.0020.026
hyperGeoTest3.0900.0563.147
interactome0.0000.0010.001
mammalAnnotationConvertor2.3380.0792.418
multiHyperGeoTest0.0060.0010.007
networkAnalysis000
networkPlot0.0010.0000.000
pairwiseGsea1.2720.0531.326
pairwiseGseaPlot0.0000.0000.001
pairwisePhenoMannWhit0.0070.0000.008
permutationPvalueCollectionGsea0.6600.0260.687
plotEnrichMap000
plotGSEA0.0000.0000.001
plotSubNet0.0000.0010.001
preprocess000
report0.0010.0000.001
reportAll0.0000.0000.001
summarize0.0010.0000.000
viewEnrichMap000
viewGSEA000
viewSubNet0.0010.0000.001
writeReportHTSA000