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Package 247/514HostnameOS / ArchBUILDCHECKBUILD BIN
HTSanalyzeR 2.6.1
Xin Wang
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 62730 / Revision: 64395
Last Changed Date: 2012-02-13 08:50:23 -0800 (Mon, 13 Feb 2012)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: HTSanalyzeR
Version: 2.6.1
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings HTSanalyzeR_2.6.1.tar.gz
StartedAt: 2012-03-24 01:00:15 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 01:05:03 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 288.8 seconds
RetCode: 0
Status:  OK 
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/HTSanalyzeR.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘HTSanalyzeR/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘HTSanalyzeR’ version ‘2.6.1’
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using R CMD build --resave-data
                               old_size new_size compress
  Biogrid_DM_Interactome.RData    326Kb    212Kb       xz
  Biogrid_DM_Mat.RData             97Kb     68Kb       xz
  KcViab_Data4Enrich.RData        117Kb     92Kb       xz
  KcViab_GSCA.RData               351Kb    239Kb       xz
  KcViab_NWA.RData                567Kb    404Kb       xz
  KcViab_Norm.RData               806Kb    528Kb       xz
  KcViab_PVals.RData              117Kb    101Kb       xz
* 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

HTSanalyzeR.Rcheck/00install.out:

* installing *source* package ‘HTSanalyzeR’ ...
** R
** data
** inst
** preparing package for lazy loading
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “connection” in package ‘graph’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
Warning in .simpleDuplicateClass(def, prev) :
  A specification for S3 class “file” in package ‘graph’ seems equivalent to one from package ‘IRanges’ and is not turning on duplicate class definitions for this class
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘HTSanalyzeR-Vignette.Rnw’ 
** testing if installed package can be loaded
locfit 1.5-6 	 2010-01-20 
Scalable Robust Estimators with High Breakdown Point (version 1.3-01)

* DONE (HTSanalyzeR)

HTSanalyzeR.Rcheck/HTSanalyzeR-Ex.timings:

nameusersystemelapsed
FDRcollectionGsea1.0560.0161.072
GOGeneSets4.0360.1284.300
GSCA-class000
HTSanalyzeR4cellHTS20.0000.0000.001
KeggGeneSets3.7970.0283.997
NWA-class000
aggregatePvals0.0040.0000.004
analyze000
analyzeGeneSetCollections000
annotationConvertor1.2400.0081.281
appendGSTerms0.0000.0000.001
biogridDataDownload000
celAnnotationConvertor1.0640.0161.133
cellHTS2OutputStatTests000
collectionGsea0.3560.0000.354
data-KcViab1.0040.0081.017
drosoAnnotationConvertor0.8160.0040.823
duplicateRemover0.0000.0000.001
getTopGeneSets000
gseaPlots0.0000.0000.001
gseaScores0.0200.0000.018
hyperGeoTest3.8040.0163.821
interactome0.0000.0000.001
mammalAnnotationConvertor2.8320.0202.865
multiHyperGeoTest0.0080.0000.006
networkAnalysis000
networkPlot0.0000.0040.000
pairwiseGsea1.2480.0081.259
pairwiseGseaPlot0.0000.0000.001
pairwisePhenoMannWhit0.0120.0000.009
permutationPvalueCollectionGsea0.3890.0040.392
plotEnrichMap000
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll000
summarize000
viewEnrichMap000
viewGSEA000
viewSubNet000
writeReportHTSA000