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BioC 2.13: CHECK report for RpsiXML on zin1

This page was generated on 2014-04-05 09:47:40 -0700 (Sat, 05 Apr 2014).

Package 622/750HostnameOS / ArchBUILDCHECKBUILD BIN
RpsiXML 2.4.0
Jitao David Zhang
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/RpsiXML
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: RpsiXML
Version: 2.4.0
Command: /home/biocbuild/bbs-2.13-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.4.0.tar.gz
StartedAt: 2014-04-05 03:42:58 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 03:45:50 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 172.7 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

* using log directory ‘/home/biocbuild/bbs-2.13-bioc/meat/RpsiXML.Rcheck’
* using R version 3.0.3 (2014-03-06)
* 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 ‘2.4.0’
* 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 ... [10s/10s] 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 ‘build’ 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 dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘AnnotationDbi’ ‘RBGL’ ‘XML’ ‘annotate’
  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 ... 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 for old-style vignette sources ... NOTE
Vignette sources only in ‘inst/doc’:
  ‘RpsiXML.Rnw’, ‘RpsiXMLApp.Rnw’
A ‘vignettes’ directory will be required as from R 3.1.0
* checking examples ... [36s/37s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
translateID 6.937  0.052   7.259
* checking for unstated dependencies in tests ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [33s/33s]
 [33s/34s] 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
  ‘/home/biocbuild/bbs-2.13-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
availableXrefs0.1000.0040.102
bait0.0760.0000.078
buildPCHypergraph2.4760.0242.505
complexName2.4360.0002.438
complexes2.6520.0082.664
eListHandler0.0240.0000.021
getAbstractByPMID0.5520.0041.156
graphSpeciesConverter3.4850.0363.536
interactionType0.2360.0040.239
interactions0.080.000.08
interactorInfo0.0760.0000.076
interactors2.5400.0322.577
null2na0.0040.0000.006
parsePsimi25Interaction2.9760.0082.989
psimi25Complex-class0.0040.0000.006
psimi25ComplexEntry-class0.0040.0000.004
psimi25Experiment-class0.0320.0000.033
psimi25Graph-class0.0040.0000.004
psimi25Hypergraph-class2.6520.0082.666
psimi25Hypergraph2GraphNEL0.0040.0000.003
psimi25Interaction-class0.0040.0000.004
psimi25InteractionEntry-class0.0040.0000.005
psimi25Interactor-class0.0040.0000.004
psimi25Source-class0.0000.0000.004
psimi25XML2Graph3.1880.0403.303
separateXMLDataByExpt0.6160.0040.669
translateID6.9370.0527.259
uniprot0.0040.0000.003
validatePSIMI250.0440.0160.110