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BioC 3.2: CHECK report for RpsiXML on zin1

This page was generated on 2015-08-24 10:47:32 -0700 (Mon, 24 Aug 2015).

Package 883/1071HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RpsiXML 2.11.0
Jitao David Zhang
Snapshot Date: 2015-08-23 16:24:14 -0700 (Sun, 23 Aug 2015)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RpsiXML
Last Changed Rev: 102594 / Revision: 107696
Last Changed Date: 2015-04-16 13:02:44 -0700 (Thu, 16 Apr 2015)
zin1 Linux (Ubuntu 14.04.2 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
perceval Mac OS X Snow Leopard (10.6.8) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
oaxaca Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RpsiXML
Version: 2.11.0
Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.11.0.tar.gz
StartedAt: 2015-08-24 03:25:33 -0700 (Mon, 24 Aug 2015)
EndedAt: 2015-08-24 03:27:37 -0700 (Mon, 24 Aug 2015)
EllapsedTime: 124.3 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.11.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/RpsiXML.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.11.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘annotate’ ‘graph’ ‘Biobase’ ‘RBGL’ ‘XML’ ‘hypergraph’
  ‘AnnotationDbi’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... [8s/8s] 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
getAbstractByPMID: no visible global function definition for ‘pubmed’
getAbstractByPMID: no visible global function definition for
  ‘buildPubMedAbst’
hyperGraphConverter: no visible global function definition for
  ‘inciMat’
list2Matrix: no visible global function definition for ‘listLen’
list2Matrix: no visible global function definition for ‘inciMat’
psimi25Hypergraph2GraphNEL: no visible global function definition for
  ‘toGraphNEL’
removeHypergraphNAnode: no visible global function definition for
  ‘hyperedges’
separateXMLDataByExpt : <anonymous>: no visible global function
  definition for ‘listLen’
edgeLabel,psimi25Hypergraph : .local: no visible global function
  definition for ‘hyperedgeLabels’
head,missing : .local: no visible binding for global variable ‘.Object’
hyperedgeNodes,Hypergraph : .local: no visible global function
  definition for ‘hyperedges’
hyperedgeNodes,Hypergraph : .local: no visible global function
  definition for ‘hyperedgeLabels’
numEdges,psimi25Hypergraph: no visible global function definition for
  ‘hyperedges’
tail,missing : .local: no visible binding for global variable ‘.Object’
translateID,psimi25Graph : .local: no visible global function
  definition for ‘combineNodes’
translateID,psimi25Graph : .local: no visible global function
  definition for ‘nodes<-’
* 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 line endings in Makefiles ... OK
* checking for GNU extensions in Makefiles ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [26s/26s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
translateID 5.046  0.024   5.071
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [26s/26s]
 [26s/27s] 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
* DONE

Status: 3 NOTEs
See
  ‘/home/biocbuild/bbs-3.2-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.


RpsiXML.Rcheck/00install.out:

* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
Note: in method for ‘head’ with signature ‘x="ANY"’: expanding the
signature to include omitted arguments in definition: x = "missing"
Note: in method for ‘tail’ with signature ‘x="ANY"’: expanding the
signature to include omitted arguments in definition: x = "missing"
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (RpsiXML)

RpsiXML.Rcheck/RpsiXML-Ex.timings:

nameusersystemelapsed
availableXrefs0.0630.0000.063
bait0.0460.0000.046
buildPCHypergraph1.7700.0161.784
complexName1.6490.0121.662
complexes2.0400.0272.089
eListHandler0.0120.0000.011
getAbstractByPMID0.6030.0160.942
graphSpeciesConverter2.2330.0122.242
interactionType0.0530.0000.052
interactions0.0540.0000.055
interactorInfo0.0570.0000.056
interactors1.7800.0241.802
null2na000
parsePsimi25Interaction2.3100.0122.321
psimi25Complex-class0.0010.0000.001
psimi25ComplexEntry-class0.0010.0000.000
psimi25Experiment-class0.0010.0000.000
psimi25Graph-class0.0010.0000.001
psimi25Hypergraph-class1.7180.0121.729
psimi25Hypergraph2GraphNEL0.0010.0000.001
psimi25Interaction-class0.0010.0000.001
psimi25InteractionEntry-class0.0010.0000.001
psimi25Interactor-class0.0010.0000.001
psimi25Source-class0.0010.0000.001
psimi25XML2Graph2.4090.0122.422
separateXMLDataByExpt0.4160.0000.415
translateID5.0460.0245.071
uniprot000
validatePSIMI250.0360.0130.054