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Package 247/516HostnameOS / ArchBUILDCHECKBUILD BIN
HTSanalyzeR 2.6.0
Xin Wang
Snapshot Date: 2012-01-08 18:22:44 -0800 (Sun, 08 Jan 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/HTSanalyzeR
Last Changed Rev: 60448 / Revision: 61898
Last Changed Date: 2011-11-17 09:31:28 -0800 (Thu, 17 Nov 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK [ 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: 2.6.0
Command: D:\biocbld\bbs-2.9-bioc\R\bin\R.exe CMD check --no-vignettes --timings --no-multiarch HTSanalyzeR_2.6.0.tar.gz
StartedAt: 2012-01-09 03:40:52 -0800 (Mon, 09 Jan 2012)
EndedAt: 2012-01-09 03:45:18 -0800 (Mon, 09 Jan 2012)
EllapsedTime: 266.5 seconds
RetCode: 0
Status:  OK  
CheckDir: HTSanalyzeR.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.9-bioc/meat/HTSanalyzeR.Rcheck'
* using R version 2.14.1 (2011-12-22)
* using platform: x86_64-pc-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.6.0'
* 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 whether package 'HTSanalyzeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... 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    251Kb       xz
  KcViab_NWA.RData                567Kb    402Kb       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
FDRcollectionGsea0.820.000.81
GOGeneSets3.450.074.73
GSCA-class000
HTSanalyzeR4cellHTS2000
KeggGeneSets4.910.065.53
NWA-class000
aggregatePvals0.020.000.02
analyze000
analyzeGeneSetCollections000
annotationConvertor0.900.011.15
appendGSTerms000
biogridDataDownload000
celAnnotationConvertor1.100.042.25
cellHTS2OutputStatTests000
collectionGsea0.360.010.37
data-KcViab0.660.020.67
drosoAnnotationConvertor0.830.000.83
duplicateRemover0.010.000.02
getTopGeneSets000
gseaPlots000
gseaScores0.050.000.04
hyperGeoTest4.250.034.29
interactome000
mammalAnnotationConvertor2.310.002.34
multiHyperGeoTest0.020.000.02
networkAnalysis000
networkPlot000
pairwiseGsea0.790.000.81
pairwiseGseaPlot000
pairwisePhenoMannWhit000
permutationPvalueCollectionGsea0.730.010.75
plotEnrichMap000
plotGSEA000
plotSubNet000
preprocess000
report000
reportAll000
summarize000
viewEnrichMap000
viewGSEA000
viewSubNet000
writeReportHTSA000