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

* 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

* 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)

name	user	system	elapsed
FDRcollectionGsea	0.82	0.00	0.81
GOGeneSets	3.45	0.07	4.73
GSCA-class	0	0	0
HTSanalyzeR4cellHTS2	0	0	0
KeggGeneSets	4.91	0.06	5.53
NWA-class	0	0	0
aggregatePvals	0.02	0.00	0.02
analyze	0	0	0
analyzeGeneSetCollections	0	0	0
annotationConvertor	0.90	0.01	1.15
appendGSTerms	0	0	0
biogridDataDownload	0	0	0
celAnnotationConvertor	1.10	0.04	2.25
cellHTS2OutputStatTests	0	0	0
collectionGsea	0.36	0.01	0.37
data-KcViab	0.66	0.02	0.67
drosoAnnotationConvertor	0.83	0.00	0.83
duplicateRemover	0.01	0.00	0.02
getTopGeneSets	0	0	0
gseaPlots	0	0	0
gseaScores	0.05	0.00	0.04
hyperGeoTest	4.25	0.03	4.29
interactome	0	0	0
mammalAnnotationConvertor	2.31	0.00	2.34
multiHyperGeoTest	0.02	0.00	0.02
networkAnalysis	0	0	0
networkPlot	0	0	0
pairwiseGsea	0.79	0.00	0.81
pairwiseGseaPlot	0	0	0
pairwisePhenoMannWhit	0	0	0
permutationPvalueCollectionGsea	0.73	0.01	0.75
plotEnrichMap	0	0	0
plotGSEA	0	0	0
plotSubNet	0	0	0
preprocess	0	0	0
report	0	0	0
reportAll	0	0	0
summarize	0	0	0
viewEnrichMap	0	0	0
viewGSEA	0	0	0
viewSubNet	0	0	0
writeReportHTSA	0	0	0