Back to the "Multiple platform build/check report" A  B  C  D  E  F  G  H  I  J  K  L  M  N  O  P  Q [R] S  T  U  V  W  X  Y  Z 

Package 533/631HostnameOS / ArchBUILDCHECKBUILD BIN
RpsiXML 2.0.0
Jitao David Zhang
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RpsiXML
Last Changed Rev: 70811 / Revision: 72575
Last Changed Date: 2012-10-28 00:37:54 -0700 (Sun, 28 Oct 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: RpsiXML
Version: 2.0.0
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.0.0.tar.gz
StartedAt: 2013-01-16 06:06:09 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 06:09:53 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 224.6 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/RpsiXML.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.0.0’
* 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 ... 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 ... OK
Examples with CPU or elapsed time > 5s
            user system elapsed
translateID 6.58   0.04   6.645
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’
 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
  ‘/loc/home/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
   ‘RpsiXML.Rnw’ 
   ‘RpsiXMLApp.Rnw’ 
** testing if installed package can be loaded

* DONE (RpsiXML)

RpsiXML.Rcheck/RpsiXML-Ex.timings:

nameusersystemelapsed
availableXrefs0.3520.0040.361
bait0.0880.0000.086
buildPCHypergraph2.9040.0282.932
complexName2.3240.0042.325
complexes3.0520.0243.078
eListHandler0.0240.0000.025
getAbstractByPMID0.9330.0081.573
graphSpeciesConverter3.6360.0563.695
interactionType0.4240.0040.426
interactions0.0840.0000.086
interactorInfo0.0880.0000.088
interactors2.6480.0442.689
null2na0.0120.0000.013
parsePsimi25Interaction3.2520.0163.270
psimi25Complex-class0.0160.0000.013
psimi25ComplexEntry-class0.0120.0000.012
psimi25Experiment-class0.0080.0000.011
psimi25Graph-class0.0080.0000.010
psimi25Hypergraph-class3.1640.0083.171
psimi25Hypergraph2GraphNEL0.0040.0000.003
psimi25Interaction-class0.0200.0040.027
psimi25InteractionEntry-class0.0160.0000.015
psimi25Interactor-class0.0120.0000.009
psimi25Source-class0.0080.0000.008
psimi25XML2Graph3.1650.0123.180
separateXMLDataByExpt0.6120.0040.617
translateID6.5800.0406.645
uniprot0.0760.0000.083
validatePSIMI250.0680.0360.305