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BioC 2.13: CHECK report for RpsiXML on moscato1

This page was generated on 2014-04-05 09:49:44 -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: rm -rf RpsiXML.buildbin-libdir && mkdir RpsiXML.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.4.0.tar.gz >RpsiXML-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.4.0.tar.gz && mv RpsiXML.buildbin-libdir/* RpsiXML.Rcheck/ && rmdir RpsiXML.buildbin-libdir
StartedAt: 2014-04-05 06:30:55 -0700 (Sat, 05 Apr 2014)
EndedAt: 2014-04-05 06:36:23 -0700 (Sat, 05 Apr 2014)
EllapsedTime: 327.9 seconds
RetCode: 0
Status:  OK  
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/RpsiXML.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 '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 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 '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
* 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
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 ...
** running examples for arch 'i386' ... [34s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
translateID 6.13   0.05    6.18
** running examples for arch 'x64' ... [44s] OK
Examples with CPU or elapsed time > 5s
            user system elapsed
translateID 6.98   0.07    7.04
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
  Running 'psimi25Source_test.R' [34s]
 [34s] OK
** running tests for arch 'x64'
  Running 'psimi25Source_test.R' [40s]
 [40s] 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/RpsiXML.Rcheck/00check.log'
for details.

RpsiXML.Rcheck/00install.out:


install for i386

* 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

install for x64

* installing *source* package 'RpsiXML' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'RpsiXML' as RpsiXML_2.4.0.zip
* DONE (RpsiXML)

RpsiXML.Rcheck/examples_i386/RpsiXML-Ex.timings:

nameusersystemelapsed
availableXrefs0.100.000.09
bait0.070.000.06
buildPCHypergraph2.350.002.35
complexName2.180.002.18
complexes2.40.02.4
eListHandler0.020.000.03
getAbstractByPMID0.550.001.14
graphSpeciesConverter3.590.083.67
interactionType0.20.00.2
interactions0.080.000.08
interactorInfo0.080.000.08
interactors2.280.032.31
null2na0.010.000.01
parsePsimi25Interaction2.650.032.68
psimi25Complex-class000
psimi25ComplexEntry-class0.010.000.02
psimi25Experiment-class000
psimi25Graph-class000
psimi25Hypergraph-class2.590.002.59
psimi25Hypergraph2GraphNEL000
psimi25Interaction-class000
psimi25InteractionEntry-class000
psimi25Interactor-class0.020.000.02
psimi25Source-class000
psimi25XML2Graph2.730.012.74
separateXMLDataByExpt0.530.020.55
translateID6.130.056.18
uniprot000
validatePSIMI25000

RpsiXML.Rcheck/examples_x64/RpsiXML-Ex.timings:

nameusersystemelapsed
availableXrefs0.100.000.11
bait0.080.010.10
buildPCHypergraph3.730.003.73
complexName2.620.022.63
complexes3.060.003.09
eListHandler0.030.000.03
getAbstractByPMID0.670.001.15
graphSpeciesConverter4.910.064.98
interactionType0.120.020.15
interactions0.120.000.13
interactorInfo0.100.000.09
interactors3.860.013.87
null2na000
parsePsimi25Interaction3.480.023.50
psimi25Complex-class000
psimi25ComplexEntry-class0.020.000.02
psimi25Experiment-class000
psimi25Graph-class000
psimi25Hypergraph-class2.840.002.84
psimi25Hypergraph2GraphNEL000
psimi25Interaction-class0.010.000.02
psimi25InteractionEntry-class000
psimi25Interactor-class000
psimi25Source-class0.020.000.01
psimi25XML2Graph4.230.014.25
separateXMLDataByExpt0.710.000.71
translateID6.980.077.04
uniprot0.010.000.02
validatePSIMI25000