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BioC 3.5: CHECK report for RpsiXML on oaxaca

This page was generated on 2017-03-04 16:36:42 -0500 (Sat, 04 Mar 2017).

Package 1106/1339HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RpsiXML 2.17.0
Jitao David Zhang
Snapshot Date: 2017-03-03 17:15:47 -0500 (Fri, 03 Mar 2017)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RpsiXML
Last Changed Rev: 122712 / Revision: 127142
Last Changed Date: 2016-10-17 15:10:43 -0400 (Mon, 17 Oct 2016)
malbec2 Linux (Ubuntu 16.04.1 LTS) / x86_64  OK  OK  OK UNNEEDED, same version exists in internal repository
tokay2 Windows Server 2012 R2 Standard / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
toluca2 Mac OS X Mavericks (10.9.5) / 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 

Summary

Package: RpsiXML
Version: 2.17.0
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RpsiXML_2.17.0.tar.gz
StartedAt: 2017-03-04 08:30:14 -0800 (Sat, 04 Mar 2017)
EndedAt: 2017-03-04 08:32:24 -0800 (Sat, 04 Mar 2017)
EllapsedTime: 129.9 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RpsiXML_2.17.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.5-bioc/meat/RpsiXML.Rcheck’
* using R Under development (unstable) (2017-02-15 r72177)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.17.0’
* 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 ... 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 ... NOTE
Warning: no function found corresponding to methods exports from ‘RpsiXML’ for: ‘initialize’

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
* 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
buildPCHypergraph: no visible global function definition for ‘new’
complexEntry2graph: no visible global function definition for ‘is’
complexEntry2graph: no visible global function definition for ‘new’
genBPGraph: no visible global function definition for ‘as’
getAbstractByPMID: no visible global function definition for ‘pubmed’
getAbstractByPMID: no visible global function definition for
  ‘buildPubMedAbst’
graphConverter: no visible global function definition for ‘is’
graphConverter: no visible global function definition for ‘as’
hyperGraphConverter: no visible global function definition for ‘is’
hyperGraphConverter: no visible global function definition for
  ‘inciMat’
interactionEntry2graph: no visible global function definition for ‘is’
interactionEntry2graph: no visible global function definition for ‘as’
list2Matrix: no visible global function definition for ‘listLen’
list2Matrix: no visible global function definition for ‘new’
list2Matrix: no visible global function definition for ‘inciMat’
parsePsimi25Complex: no visible global function definition for ‘new’
parseXmlAttribute: no visible global function definition for ‘new’
parseXmlComplexNode: no visible global function definition for ‘new’
parseXmlEntryNode: no visible global function definition for ‘new’
parseXmlEntryNodeSet: no visible global function definition for ‘new’
parseXmlExperimentNode: no visible global function definition for ‘new’
parseXmlInteractionNode: no visible global function definition for
  ‘new’
parseXmlInteractorNode: no visible global function definition for ‘new’
psimi25Hypergraph2GraphNEL: no visible global function definition for
  ‘toGraphNEL’
psimi25Hypergraph2GraphNEL: no visible global function definition for
  ‘as’
removeHypergraphNAnode: no visible global function definition for
  ‘hyperedges’
separateXMLDataByExpt : <anonymous>: no visible global function
  definition for ‘listLen’
separateXMLDataByExpt : <anonymous>: no visible global function
  definition for ‘as’
validatePSIMI25: no visible global function definition for
  ‘download.file’
edgeLabel,psimi25Hypergraph: no visible global function definition for
  ‘hyperedgeLabels’
head,missing: no visible binding for global variable ‘.Object’
hyperedgeNodes,Hypergraph: no visible global function definition for
  ‘hyperedges’
hyperedgeNodes,Hypergraph: no visible global function definition for
  ‘hyperedgeLabels’
initialize,psimi25Hypergraph: no visible global function definition for
  ‘callNextMethod’
interactorInfo,list: no visible binding for global variable ‘is’
interactorInfo,list: no visible global function definition for ‘slot’
numEdges,psimi25Hypergraph: no visible global function definition for
  ‘hyperedges’
revInciMat,matrix: no visible global function definition for ‘new’
show,psimi25Graph: no visible global function definition for ‘as’
tail,missing: no visible binding for global variable ‘.Object’
translateID,list: no visible binding for global variable ‘is’
translateID,psimi25Graph: no visible global function definition for
  ‘combineNodes’
translateID,psimi25Graph: no visible global function definition for
  ‘nodes<-’
Undefined global functions or variables:
  .Object as buildPubMedAbst callNextMethod combineNodes download.file
  hyperedgeLabels hyperedges inciMat is listLen new nodes<- pubmed slot
  toGraphNEL
Consider adding
  importFrom("methods", "as", "callNextMethod", "is", "new", "slot")
  importFrom("utils", "download.file")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* 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 ... OK
* 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK
* DONE

Status: 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.5-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
availableXrefs0.3330.0020.334
bait0.1690.0110.180
buildPCHypergraph1.3110.0121.322
complexName1.2710.0101.282
complexes1.2590.0221.281
eListHandler0.0070.0000.008
getAbstractByPMID0.2950.0130.955
graphSpeciesConverter2.3970.0642.575
interactionType0.0370.0010.039
interactions0.0420.0010.044
interactorInfo0.0380.0000.038
interactors1.2370.0341.273
null2na0.0010.0000.000
parsePsimi25Interaction1.3540.0161.370
psimi25Complex-class0.0020.0000.002
psimi25ComplexEntry-class0.0010.0000.000
psimi25Experiment-class0.0000.0000.001
psimi25Graph-class0.0010.0000.001
psimi25Hypergraph-class1.2060.0181.224
psimi25Hypergraph2GraphNEL0.0010.0000.001
psimi25Interaction-class0.0010.0000.001
psimi25InteractionEntry-class0.0010.0010.000
psimi25Interactor-class0.0000.0000.001
psimi25Source-class0.0010.0000.001
psimi25XML2Graph1.4700.0121.482
separateXMLDataByExpt0.3750.0090.384
translateID3.110.043.15
uniprot000
validatePSIMI250.0390.0090.116