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Package 566/671HostnameOS / ArchBUILDCHECKBUILD BIN
RpsiXML 2.2.0
Jitao David Zhang
Snapshot Date: 2013-04-30 17:01:37 -0700 (Tue, 30 Apr 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_12/madman/Rpacks/RpsiXML
Last Changed Rev: 75263 / Revision: 76155
Last Changed Date: 2013-04-03 14:32:27 -0700 (Wed, 03 Apr 2013)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK 
pelham Mac OS X Snow Leopard (10.6.8) / x86_64  OK [ OK ] OK 

Summary

Package: RpsiXML
Version: 2.2.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.2.0.tar.gz
StartedAt: 2013-05-01 10:33:32 -0700 (Wed, 01 May 2013)
EndedAt: 2013-05-01 10:38:25 -0700 (Wed, 01 May 2013)
EllapsedTime: 293.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/RpsiXML.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '2.2.0'
* 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 for sufficient/correct file permissions ... OK
* checking whether package 'RpsiXML' can be installed ... [18s/21s] OK
* checking installed package size ... NOTE
  installed size is 33.8Mb
  sub-directories of 1Mb or more:
    extdata  32.7Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* 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
* 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 ... OK
* 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 installed files from 'inst/doc' ... NOTE
The following files should probably not be installed:
  'underscore.sty'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... [54s/56s] OK
Examples with CPU or elapsed time > 5s
                       user system elapsed
translateID           9.231  0.134   9.430
graphSpeciesConverter 4.990  0.146   5.249
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running 'psimi25Source_test.R' [47s/47s]
 [47s/48s] 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 were 2 notes.
See
  '/Users/biocbuild/bbs-2.12-bioc/meat/RpsiXML.Rcheck/00check.log'
for details.

RpsiXML.Rcheck/00install.out:

* installing *source* package 'RpsiXML' ...
** R
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (RpsiXML)

RpsiXML.Rcheck/RpsiXML-Ex.timings:

nameusersystemelapsed
availableXrefs0.4110.0140.426
bait0.1040.0070.112
buildPCHypergraph3.9120.0684.001
complexName3.5030.0393.565
complexes3.6660.0793.797
eListHandler0.0380.0040.041
getAbstractByPMID0.8140.0331.501
graphSpeciesConverter4.9900.1465.249
interactionType0.4390.0260.482
interactions0.1270.0100.137
interactorInfo0.1100.0070.127
interactors3.5270.1133.669
null2na0.0080.0040.012
parsePsimi25Interaction4.0630.0584.144
psimi25Complex-class0.0140.0050.019
psimi25ComplexEntry-class0.0080.0030.011
psimi25Experiment-class0.0080.0020.011
psimi25Graph-class0.0090.0020.012
psimi25Hypergraph-class3.6230.0503.779
psimi25Hypergraph2GraphNEL0.0080.0020.010
psimi25Interaction-class0.0160.0040.019
psimi25InteractionEntry-class0.0090.0050.014
psimi25Interactor-class0.0070.0030.011
psimi25Source-class0.0060.0030.010
psimi25XML2Graph4.2730.0544.367
separateXMLDataByExpt0.8760.0240.906
translateID9.2310.1349.430
uniprot0.0120.0020.015
validatePSIMI250.1080.0340.205