BioC 2.13: CHECK report for HTSanalyzeR on moscato1
This page was generated on 2014-04-05 09:50:08 -0700 (Sat, 05 Apr 2014).
HTSanalyzeR 2.14.0
Xin Wang
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/HTSanalyzeR | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
| Package: HTSanalyzeR
|
| Version: 2.14.0
|
| Command: rm -rf HTSanalyzeR.buildbin-libdir && mkdir HTSanalyzeR.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=HTSanalyzeR.buildbin-libdir HTSanalyzeR_2.14.0.tar.gz >HTSanalyzeR-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=HTSanalyzeR.buildbin-libdir --install="check:HTSanalyzeR-install.out" --force-multiarch --no-vignettes --timings HTSanalyzeR_2.14.0.tar.gz && mv HTSanalyzeR.buildbin-libdir/* HTSanalyzeR.Rcheck/ && rmdir HTSanalyzeR.buildbin-libdir
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| StartedAt: 2014-04-05 04:35:38 -0700 (Sat, 05 Apr 2014)
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| EndedAt: 2014-04-05 04:42:36 -0700 (Sat, 05 Apr 2014)
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| EllapsedTime: 417.9 seconds
|
| RetCode: 0
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| Status: OK
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| CheckDir: HTSanalyzeR.Rcheck
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| Warnings: 0
|
Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/HTSanalyzeR.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 'HTSanalyzeR/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'HTSanalyzeR' version '2.14.0'
* 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 'HTSanalyzeR' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking 'build' directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
'igraph'
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
Package in Depends field not imported from: 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
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
File 'HTSanalyzeR/R/zzz.R':
.onLoad calls:
packageStartupMessage("/////////////////////////////////////////////////////////////////////////////\n\n//------------------ Thanks for using HTSanalyzeR -------------------//\n \n//------------please use function changes() to see new changes-------------//\n\n//------------please report any bug to xinwang2hms@gmail.com---------------//\n\n/////////////////////////////////////////////////////////////////////////////\n", appendLF = FALSE)
See section 'Good practice' in '?.onAttach'.
* 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 installed files from 'inst/doc' ... OK
* checking for old-style vignette sources ... NOTE
Vignette sources only in 'inst/doc':
'HTSanalyzeR-Vignette.Rnw'
A 'vignettes' directory will be required as from R 3.1.0
* checking examples ...
** running examples for arch 'i386' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
celAnnotationConvertor 2.54 0.09 5.02
** running examples for arch 'x64' ... [37s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
NOTE: There were 4 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/HTSanalyzeR.Rcheck/00check.log'
for details.
HTSanalyzeR.Rcheck/00install.out:
install for i386
* installing *source* package 'HTSanalyzeR' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'HTSanalyzeR' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'HTSanalyzeR' as HTSanalyzeR_2.14.0.zip
* DONE (HTSanalyzeR)
HTSanalyzeR.Rcheck/examples_i386/HTSanalyzeR-Ex.timings:
| name | user | system | elapsed
|
| FDRcollectionGsea | 0.85 | 0.01 | 0.86 |
|
| GOGeneSets | 2.41 | 0.11 | 4.46 |
|
| GSCA-class | 0.00 | 0.02 | 0.01 |
|
| HTSanalyzeR4cellHTS2 | 0.02 | 0.00 | 0.02 |
|
| KeggGeneSets | 3.32 | 0.03 | 3.40 |
|
| NWA-class | 0.01 | 0.00 | 0.01 |
|
| aggregatePvals | 0.02 | 0.00 | 0.02 |
|
| analyze | 0.02 | 0.00 | 0.01 |
|
| analyzeGeneSetCollections | 0 | 0 | 0 |
|
| annotationConvertor | 1.23 | 0.00 | 1.99 |
|
| appendGSTerms | 0.02 | 0.00 | 0.02 |
|
| biogridDataDownload | 0 | 0 | 0 |
|
| celAnnotationConvertor | 2.54 | 0.09 | 5.02 |
|
| cellHTS2OutputStatTests | 0.02 | 0.00 | 0.01 |
|
| changes | 0.02 | 0.00 | 0.01 |
|
| collectionGsea | 1.17 | 0.00 | 1.17 |
|
| data-KcViab | 1.61 | 0.02 | 1.72 |
|
| drosoAnnotationConvertor | 1.73 | 0.00 | 1.73 |
|
| duplicateRemover | 0.02 | 0.00 | 0.01 |
|
| getTopGeneSets | 0.05 | 0.00 | 0.05 |
|
| gseaPlots | 0.02 | 0.00 | 0.01 |
|
| gseaScores | 0.08 | 0.00 | 0.08 |
|
| hyperGeoTest | 3.85 | 0.01 | 3.87 |
|
| interactome | 0.03 | 0.00 | 0.03 |
|
| mammalAnnotationConvertor | 2.14 | 0.02 | 2.16 |
|
| multiHyperGeoTest | 0.05 | 0.00 | 0.04 |
|
| networkAnalysis | 0.02 | 0.00 | 0.01 |
|
| networkPlot | 0.03 | 0.00 | 0.04 |
|
| pairwiseGsea | 1.53 | 0.00 | 1.52 |
|
| pairwiseGseaPlot | 0.02 | 0.00 | 0.02 |
|
| pairwisePhenoMannWhit | 0.03 | 0.00 | 0.03 |
|
| permutationPvalueCollectionGsea | 0.48 | 0.00 | 0.49 |
|
| plotEnrichMap | 0.02 | 0.00 | 0.01 |
|
| plotGSEA | 0.06 | 0.00 | 0.06 |
|
| plotSubNet | 0.05 | 0.00 | 0.04 |
|
| preprocess | 0.05 | 0.00 | 0.05 |
|
| report | 0.04 | 0.00 | 0.05 |
|
| reportAll | 0.03 | 0.00 | 0.04 |
|
| summarize | 0.04 | 0.00 | 0.03 |
|
| viewEnrichMap | 0.03 | 0.00 | 0.03 |
|
| viewGSEA | 0.01 | 0.00 | 0.01 |
|
| viewSubNet | 0.01 | 0.00 | 0.01 |
|
| writeReportHTSA | 0.02 | 0.00 | 0.01 |
|
HTSanalyzeR.Rcheck/examples_x64/HTSanalyzeR-Ex.timings:
| name | user | system | elapsed
|
| FDRcollectionGsea | 0.89 | 0.02 | 0.91 |
|
| GOGeneSets | 3.60 | 0.11 | 3.81 |
|
| GSCA-class | 0.00 | 0.01 | 0.01 |
|
| HTSanalyzeR4cellHTS2 | 0.02 | 0.00 | 0.02 |
|
| KeggGeneSets | 4.15 | 0.02 | 4.16 |
|
| NWA-class | 0.03 | 0.00 | 0.03 |
|
| aggregatePvals | 0.02 | 0.00 | 0.02 |
|
| analyze | 0.02 | 0.00 | 0.03 |
|
| analyzeGeneSetCollections | 0.02 | 0.00 | 0.02 |
|
| annotationConvertor | 1.30 | 0.01 | 1.31 |
|
| appendGSTerms | 0 | 0 | 0 |
|
| biogridDataDownload | 0 | 0 | 0 |
|
| celAnnotationConvertor | 2.12 | 0.03 | 2.15 |
|
| cellHTS2OutputStatTests | 0 | 0 | 0 |
|
| changes | 0 | 0 | 0 |
|
| collectionGsea | 0.28 | 0.00 | 0.28 |
|
| data-KcViab | 0.93 | 0.02 | 0.95 |
|
| drosoAnnotationConvertor | 1.57 | 0.01 | 1.59 |
|
| duplicateRemover | 0.03 | 0.00 | 0.03 |
|
| getTopGeneSets | 0.03 | 0.02 | 0.05 |
|
| gseaPlots | 0.02 | 0.02 | 0.03 |
|
| gseaScores | 0.09 | 0.00 | 0.10 |
|
| hyperGeoTest | 4.56 | 0.03 | 4.58 |
|
| interactome | 0.01 | 0.00 | 0.02 |
|
| mammalAnnotationConvertor | 3.11 | 0.03 | 3.14 |
|
| multiHyperGeoTest | 0.03 | 0.00 | 0.03 |
|
| networkAnalysis | 0.03 | 0.00 | 0.03 |
|
| networkPlot | 0.03 | 0.00 | 0.03 |
|
| pairwiseGsea | 0.75 | 0.01 | 0.77 |
|
| pairwiseGseaPlot | 0.02 | 0.00 | 0.01 |
|
| pairwisePhenoMannWhit | 0.03 | 0.00 | 0.03 |
|
| permutationPvalueCollectionGsea | 0.39 | 0.00 | 0.39 |
|
| plotEnrichMap | 0.02 | 0.00 | 0.01 |
|
| plotGSEA | 0.02 | 0.00 | 0.02 |
|
| plotSubNet | 0.02 | 0.00 | 0.02 |
|
| preprocess | 0.02 | 0.01 | 0.03 |
|
| report | 0.02 | 0.00 | 0.02 |
|
| reportAll | 0.03 | 0.00 | 0.03 |
|
| summarize | 0.02 | 0.00 | 0.02 |
|
| viewEnrichMap | 0.01 | 0.00 | 0.01 |
|
| viewGSEA | 0.02 | 0.00 | 0.02 |
|
| viewSubNet | 0 | 0 | 0 |
|
| writeReportHTSA | 0.02 | 0.00 | 0.02 |
|