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BioC 3.4: CHECK report for RpsiXML on zin1

This page was generated on 2016-09-21 03:36:38 -0700 (Wed, 21 Sep 2016).

Package 1048/1257HostnameOS / ArchINSTALLBUILDCHECKBUILD BIN
RpsiXML 2.15.0
Jitao David Zhang
Snapshot Date: 2016-09-19 19:15:14 -0700 (Mon, 19 Sep 2016)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RpsiXML
Last Changed Rev: 117081 / Revision: 121152
Last Changed Date: 2016-05-03 14:30:44 -0700 (Tue, 03 May 2016)
zin1 Linux (Ubuntu 16.04 LTS) / x86_64  OK  OK [ OK ]UNNEEDED, same version exists in internal repository
moscato1 Windows Server 2008 R2 Standard (64-bit) / x64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository
morelia Mac OS X Mavericks (10.9.5) / x86_64  OK  OK  OK  OK UNNEEDED, same version exists in internal repository

Summary

Package: RpsiXML
Version: 2.15.0
Command: /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.15.0.tar.gz
StartedAt: 2016-09-20 12:02:44 -0700 (Tue, 20 Sep 2016)
EndedAt: 2016-09-20 12:04:44 -0700 (Tue, 20 Sep 2016)
EllapsedTime: 120.1 seconds
RetCode: 0
Status:  OK 
CheckDir: RpsiXML.Rcheck
Warnings: 0

Command output

##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.4-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.15.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.4-bioc/meat/RpsiXML.Rcheck’
* using R version 3.3.1 (2016-06-21)
* 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 ‘2.15.0’
* 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
  ‘/home/biocbuild/bbs-3.4-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
availableXrefs0.1880.0000.190
bait0.0440.0000.045
buildPCHypergraph1.6920.0041.704
complexName1.7480.0001.759
complexes1.9720.0041.976
eListHandler0.0120.0040.020
getAbstractByPMID0.4200.0201.093
graphSpeciesConverter2.3440.0122.365
interactionType0.0600.0000.061
interactions0.0600.0040.061
interactorInfo0.0560.0000.058
interactors1.8520.0201.873
null2na000
parsePsimi25Interaction2.3120.0122.326
psimi25Complex-class0.0040.0000.002
psimi25ComplexEntry-class0.0040.0000.002
psimi25Experiment-class0.0000.0000.001
psimi25Graph-class0.0000.0000.001
psimi25Hypergraph-class1.8880.0041.893
psimi25Hypergraph2GraphNEL000
psimi25Interaction-class0.0000.0000.001
psimi25InteractionEntry-class0.0000.0000.001
psimi25Interactor-class0.0000.0040.001
psimi25Source-class0.0000.0000.001
psimi25XML2Graph2.3600.0082.367
separateXMLDataByExpt0.4440.0000.441
translateID4.5080.0084.517
uniprot0.0000.0000.001
validatePSIMI250.0240.0200.068