Multiple platform build/check report for BioC 3.6 - CHECK report for RpsiXML on tokay1

Package: RpsiXML

Version: 2.20.0

Command: rm -rf RpsiXML.buildbin-libdir RpsiXML.Rcheck && mkdir RpsiXML.buildbin-libdir RpsiXML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.20.0.tar.gz >RpsiXML.Rcheck\00install.out 2>&1 && cp RpsiXML.Rcheck\00install.out RpsiXML-install.out && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.20.0.tar.gz

StartedAt: 2018-04-12 02:51:19 -0400 (Thu, 12 Apr 2018)

EndedAt: 2018-04-12 02:54:30 -0400 (Thu, 12 Apr 2018)

EllapsedTime: 191.3 seconds

RetCode: 0

Status: OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

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###
### Running command:
###
###   rm -rf RpsiXML.buildbin-libdir RpsiXML.Rcheck && mkdir RpsiXML.buildbin-libdir RpsiXML.Rcheck && C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.20.0.tar.gz >RpsiXML.Rcheck\00install.out 2>&1 && cp RpsiXML.Rcheck\00install.out RpsiXML-install.out  &&  C:\Users\biocbuild\bbs-3.6-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.20.0.tar.gz
###
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* using log directory 'C:/Users/biocbuild/bbs-3.6-bioc/meat/RpsiXML.Rcheck'
* using R version 3.4.4 (2018-03-15)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'RpsiXML/DESCRIPTION' ... OK
* this is package 'RpsiXML' version '2.20.0'
* 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 whether package 'RpsiXML' can be installed ... OK
* checking installed package size ... NOTE
  installed size is 33.9Mb
  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 ... 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
* 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 ... 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
  Running 'psimi25Source_test.R'
 OK
** running tests for arch 'x64' ...
  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: 5 NOTEs
See
  'C:/Users/biocbuild/bbs-3.6-bioc/meat/RpsiXML.Rcheck/00check.log'
for details.


install for i386

* installing *source* package 'RpsiXML' ...
** R
** inst
** preparing package for lazy loading
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
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
  converting help for package 'RpsiXML'
    finding HTML links ... done
    BIOGRID.PSIMI25                         html  
    availableXrefs-methods                  html  
    availableXrefs                          html  
    bait                                    html  
    buildPCHypergraph                       html  
    complexName                             html  
    complexes                               html  
    eListHandler                            html  
    getAbstractByPMID                       html  
    graphSpeciesConverter                   html  
    interactionType                         html  
    interactions                            html  
    interactorInfo-methods                  html  
    interactorInfo                          html  
    interactors                             html  
    list2Matrix                             html  
    null2na                                 html  
    numInteractions-methods                 html  
    parsePsimi25Interaction                 html  
    psimi25Attribute-class                  html  
    psimi25Complex-class                    html  
    psimi25ComplexEntry-class               html  
    psimi25Experiment-class                 html  
    psimi25Graph-class                      html  
    psimi25Hypergraph-class                 html  
    psimi25Hypergraph2GraphNEL              html  
    psimi25Interaction-class                html  
    psimi25InteractionEntry-class           html  
    psimi25Interactor-class                 html  
    psimi25Source-class                     html  
    psimi25XML2Graph                        html  
    separateXMLDataByExpt                   html  
    sourceId-methods                        html  
    taxId-methods                           html  
    translateID-methods                     html  
    translateID                             html  
    uniprot-methods                         html  
    uniprot                                 html  
    validatePSIMI25                         html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
In R CMD INSTALL

install for x64

* installing *source* package 'RpsiXML' ...
** testing if installed package can be loaded
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'
* MD5 sums
packaged installation of 'RpsiXML' as RpsiXML_2.20.0.zip
* DONE (RpsiXML)
In R CMD INSTALL
In R CMD INSTALL


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: i386-w64-mingw32/i386 (32-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RpsiXML)
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: RBGL
Loading required package: hypergraph
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'

Attaching package: 'RpsiXML'

The following object is masked from 'package:IRanges':

    members

> xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
> 
> ## HPRD: schema check passed
> hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
> hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: .........
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
......
> hprdInteractors <- interactors(hprdSet)
> hprdInteractorInfo <- interactorInfo(hprdSet)
> pubmedID(hprdSet)
[1] "9443898"  "7738346"  "9606214"  "11790773" "15140227" "12707304"
> 
> ## BiOGRID: schema check failed, trivial
> gridxml <- file.path(xmlDir, "biogrid_200804_test.xml")
> gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ...
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
.....
> 
> ## large files
> gridLargexml <- file.path(xmlDir, "biogrid_2008_test_large.xml")
> gridHumanxml <- file.path(xmlDir, "biogrid_2008_test_human.xml")
> 
> if(file.exists(gridLargexml)) {
+   Rprof("gridLarge.prof")
+   gridLargeSet <- parsePsimi25Interaction(gridLargexml, BIOGRID.PSIMI25, verbose=TRUE)
+   Rprof(NULL)
+ }
> if(file.exists(gridHumanxml)){
+   Rprof("gridHuman.prof")
+   gridHumanSet <- parsePsimi25Interaction(gridHumanxml, BIOGRID.PSIMI25)
+   Rprof(NULL)
+ }
> 
> ## MINT: schema check passed
> mintxml <- file.path(xmlDir, "mint_200711_test.xml")
> mintSet <- parsePsimi25Interaction(mintxml, MINT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  6% ==>
  12% =====>
  19% ========>
  25% ==========>
  31% ============>
  38% ===============>
  44% ==================>
  50% ====================>
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  62% =========================>
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  75% ==============================>
  81% ================================>
  88% ===================================>
  94% ======================================>
  100% ========================================>
  Parsing interactions:
.................
> 
> ## IntAct: schema check passed
> intactxml <- file.path(xmlDir, "intact_2008_test.xml")
> intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
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  Parsing interactions:
.............................................................................................
> intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
  26% ==========>
  29% ============>
  32% =============>
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  97% =======================================>
  100% ========================================>
  Parsing interactions:
.............................................................................................
> intactGraphNew <- translateID(intactGraph,"sourceId")## translate the nodes of the graph to another identifier
> intactTestInteraction <- interactions(intactSet)[[1]]
> bait(intactTestInteraction)
[1] "A4JYL6"
> prey(intactTestInteraction)
[1] "A4JYH2"
> participant(intactTestInteraction)
  A4JYH2   A4JYL6 
"A4JYH2" "A4JYL6" 
> inhibitor(intactTestInteraction)
[1] NA
> neutralComponent(intactTestInteraction)
[1] NA
> pubmedID(intactTestInteraction)
[1] "18296487"
> intactTestInteractor <- interactors(intactSet)[[1]]
> availableXrefs(intactTestInteractor)
[1] "sourceId"  "uniprotkb" "intact"   
> 
> ## which cross references does the set provide?
> intactXrefs <- availableXrefs(intactSet)
> ## which references exist for every interactor?
> intactXrefIns <- availableXrefs(intactSet, intersect=TRUE)
> 
> intactSetInteractors <- interactors(intactSet)
> intactXrefExample <- xref(intactSetInteractors[[1]])
> translateID(intactSetInteractors,"intact")
       A4JYH2        A4JYL6        Q7ZU88        Q5J1R9        Q7SX76 
"EBI-1579530" "EBI-1579616" "EBI-1579427" "EBI-1579627" "EBI-1579511" 
       A4JYK9        A4JYF7        A4JYL8        A4JYI5        A4JYL3 
"EBI-1579400" "EBI-1579578" "EBI-1579370" "EBI-1579373" "EBI-1579353" 
       A4JYM3        A3KPA0        A0S0K7        A4JYP5        A4JYG4 
"EBI-1579304" "EBI-1579361" "EBI-1579594" "EBI-1579664" "EBI-1579266" 
       A4JYF6        Q90YM1        A4JYG2        A4JYG3        P09326 
"EBI-1579619" "EBI-1579680" "EBI-1579332" "EBI-1579335"  "EBI-714770" 
       Q9BZW8        P04218        A4JYD4        Q6NW92        A4JYD8 
"EBI-1580565"  "EBI-915817" "EBI-1579591" "EBI-1579483" "EBI-1579656" 
       A4JYG1        A2CF10        A4JYF3        Q5W433        Q90413 
"EBI-1579667" "EBI-1579611" "EBI-1579465" "EBI-1579381" "EBI-1579413" 
       A4JYS0 
"EBI-1579603" 
> translateID(intactSetInteractors[[1]],"intact")
[1] "EBI-1579530"
> 
> intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
> intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)
> intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")
> translateID(intactComplexGraph, "intact", "P49432")
[1] "EBI-917663"
> translateID(intactComplexGraph, "intact", NA)
         <NA>          <NA>          <NA>          <NA>          <NA> 
"EBI-1163494"  "EBI-967760" "EBI-1225105" "EBI-1225103"  "EBI-847690" 
> 
> complexSample <- complexes(intactComplexSet)[[2]]
> complexName(complexSample)
[1] "BAD:BCL-2 heterodimer"
> attributesList(complexSample)
[[1]]
curated-complex: BH3 domain-containing BAD interacts with and inhibits anti-apoptotic BCL-2. May act to prevent BCl-2 from sequestering BID and other pro-apoptotic molecules.

[[2]]
complex-synonym: BAD:BCL-2; BAD:BCL2; BCL-2:BAD; BCL2:BAD;

[[3]]
kd: 0.0

> members(complexSample)
  sourceId uniprotId multiplicity
4        4    P10415            1
8        8    Q92934            1
> 
> ## DIP: schema check failed, namespace not unique, modified
> dipxml <- file.path(xmlDir, "dip_2008_test.xml")
> dipSet <- parsePsimi25Interaction(dipxml, DIP.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  3% =>
  5% ==>
  8% ===>
  10% ====>
  13% =====>
  15% ======>
  18% =======>
  20% ========>
  23% =========>
  25% ==========>
  28% ===========>
  30% ============>
  33% =============>
  35% ==============>
  38% ===============>
  40% ================>
  43% =================>
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  58% =======================>
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  86% ==================================>
  88% ===================================>
  91% ====================================>
  93% =====================================>
  96% ======================================>
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  100% ========================================>
  Parsing interactions:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> dipInteractions <- interactions(dipSet)
> dipInteractionTypes <- sapply(dipInteractions, interactionType)
> stopifnot(!any(is.na(dipInteractionTypes)))
> 
> ## MatrixDB
> matrixdbxml <- file.path(xmlDir, "matrixdb_20080609.xml")
> matrixdbSet <- parsePsimi25Interaction(matrixdbxml, MATRIXDB.PSIMI25)
141 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  50% ====================>
  100% ========================================>
  Parsing interactions:
.
> 
> ## MIPS: schema check failed
> ##mipsxml <- file.path(xmlDir, "mips_2007_test.xml")
> ##mipsSet <- parsePsimi25Interaction(mipsxml, MIPS.PSIMI25) ## needs implementation
> 
> ## CORUM:
> corumxml <- file.path(xmlDir,"corumPsimi")
> if(file.exists(corumxml)) {
+ corumSet <- parsePsimi25Interaction(corumxml,CORUM.PSIMI25, verbose=FALSE)
+ }
> 
> ##############################
> ## Validating PSI-MI 2.5 Files
> ##############################
> #okFile <- system.file("extdata/psi25files/intact_2008_test.xml",
> #                      package="RpsiXML")
> #errorFile <- system.file("extdata/psi25files/mips_2007_test.xml",
> #                         package="RpsiXML")
> #mif25Schema <- system.file("extdata/schemas/MIF25.xsd",package="RpsiXML")
> #stopifnot(file.exists(okFile) &&
> #          file.exists(errorFile) &&
> #          file.exists(mif25Schema))
> #
> #validatePSIMI25(okFile)
> #validatePSIMI25(errorFile)
> #validatePSIMI25(errorFile, ignore.stderr=FALSE)
> 
> 
> proc.time()
   user  system elapsed 
  14.65    0.20   14.84


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

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You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> library(RpsiXML)
Loading required package: annotate
Loading required package: AnnotationDbi
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

The following objects are masked from 'package:parallel':

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from 'package:stats':

    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

The following object is masked from 'package:base':

    expand.grid

Loading required package: XML
Loading required package: graph

Attaching package: 'graph'

The following object is masked from 'package:XML':

    addNode

Loading required package: RBGL
Loading required package: hypergraph
No methods found in package 'Biobase' for request: 'listlen' when loading 'RpsiXML'
No methods found in package 'annotate' for requests: 'pubmed', 'buildPubMedAbst' when loading 'RpsiXML'

Attaching package: 'RpsiXML'

The following object is masked from 'package:IRanges':

    members

> xmlDir <- system.file("/extdata/psi25files",package="RpsiXML")
> 
> ## HPRD: schema check passed
> hprdxml <- file.path(xmlDir, "hprd_200709_test.xml")
> hprdSet <- parsePsimi25Interaction(hprdxml, HPRD.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: .........
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
......
> hprdInteractors <- interactors(hprdSet)
> hprdInteractorInfo <- interactorInfo(hprdSet)
> pubmedID(hprdSet)
[1] "9443898"  "7738346"  "9606214"  "11790773" "15140227" "12707304"
> 
> ## BiOGRID: schema check failed, trivial
> gridxml <- file.path(xmlDir, "biogrid_200804_test.xml")
> gridSet <- parsePsimi25Interaction(gridxml, BIOGRID.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ...
  Parsing interactors:

  14% ======>
  29% ============>
  43% =================>
  57% =======================>
  71% ============================>
  86% ==================================>
  100% ========================================>
  Parsing interactions:
.....
> 
> ## large files
> gridLargexml <- file.path(xmlDir, "biogrid_2008_test_large.xml")
> gridHumanxml <- file.path(xmlDir, "biogrid_2008_test_human.xml")
> 
> if(file.exists(gridLargexml)) {
+   Rprof("gridLarge.prof")
+   gridLargeSet <- parsePsimi25Interaction(gridLargexml, BIOGRID.PSIMI25, verbose=TRUE)
+   Rprof(NULL)
+ }
> if(file.exists(gridHumanxml)){
+   Rprof("gridHuman.prof")
+   gridHumanSet <- parsePsimi25Interaction(gridHumanxml, BIOGRID.PSIMI25)
+   Rprof(NULL)
+ }
> 
> ## MINT: schema check passed
> mintxml <- file.path(xmlDir, "mint_200711_test.xml")
> mintSet <- parsePsimi25Interaction(mintxml, MINT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  6% ==>
  12% =====>
  19% ========>
  25% ==========>
  31% ============>
  38% ===============>
  44% ==================>
  50% ====================>
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  81% ================================>
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  100% ========================================>
  Parsing interactions:
.................
> 
> ## IntAct: schema check passed
> intactxml <- file.path(xmlDir, "intact_2008_test.xml")
> intactSet <- parsePsimi25Interaction(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
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  Parsing interactions:
.............................................................................................
> intactGraph <- psimi25XML2Graph(intactxml, INTACT.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: ..
  Parsing interactors:

  3% =>
  6% ==>
  10% ====>
  13% =====>
  16% ======>
  19% ========>
  23% =========>
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  29% ============>
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  81% ================================>
  84% ==================================>
  87% ===================================>
  90% ====================================>
  94% ======================================>
  97% =======================================>
  100% ========================================>
  Parsing interactions:
.............................................................................................
> intactGraphNew <- translateID(intactGraph,"sourceId")## translate the nodes of the graph to another identifier
> intactTestInteraction <- interactions(intactSet)[[1]]
> bait(intactTestInteraction)
[1] "A4JYL6"
> prey(intactTestInteraction)
[1] "A4JYH2"
> participant(intactTestInteraction)
  A4JYH2   A4JYL6 
"A4JYH2" "A4JYL6" 
> inhibitor(intactTestInteraction)
[1] NA
> neutralComponent(intactTestInteraction)
[1] NA
> pubmedID(intactTestInteraction)
[1] "18296487"
> intactTestInteractor <- interactors(intactSet)[[1]]
> availableXrefs(intactTestInteractor)
[1] "sourceId"  "uniprotkb" "intact"   
> 
> ## which cross references does the set provide?
> intactXrefs <- availableXrefs(intactSet)
> ## which references exist for every interactor?
> intactXrefIns <- availableXrefs(intactSet, intersect=TRUE)
> 
> intactSetInteractors <- interactors(intactSet)
> intactXrefExample <- xref(intactSetInteractors[[1]])
> translateID(intactSetInteractors,"intact")
       A4JYH2        A4JYL6        Q7ZU88        Q5J1R9        Q7SX76 
"EBI-1579530" "EBI-1579616" "EBI-1579427" "EBI-1579627" "EBI-1579511" 
       A4JYK9        A4JYF7        A4JYL8        A4JYI5        A4JYL3 
"EBI-1579400" "EBI-1579578" "EBI-1579370" "EBI-1579373" "EBI-1579353" 
       A4JYM3        A3KPA0        A0S0K7        A4JYP5        A4JYG4 
"EBI-1579304" "EBI-1579361" "EBI-1579594" "EBI-1579664" "EBI-1579266" 
       A4JYF6        Q90YM1        A4JYG2        A4JYG3        P09326 
"EBI-1579619" "EBI-1579680" "EBI-1579332" "EBI-1579335"  "EBI-714770" 
       Q9BZW8        P04218        A4JYD4        Q6NW92        A4JYD8 
"EBI-1580565"  "EBI-915817" "EBI-1579591" "EBI-1579483" "EBI-1579656" 
       A4JYG1        A2CF10        A4JYF3        Q5W433        Q90413 
"EBI-1579667" "EBI-1579611" "EBI-1579465" "EBI-1579381" "EBI-1579413" 
       A4JYS0 
"EBI-1579603" 
> translateID(intactSetInteractors[[1]],"intact")
[1] "EBI-1579530"
> 
> intactComplexxml <- file.path(xmlDir,"intact_complexSample.xml")
> intactComplexSet <- parsePsimi25Complex(intactComplexxml, INTACT.PSIMI25)
> intactComplexGraph <- psimi25XML2Graph(intactComplexxml, INTACT.PSIMI25, type="complex")
> translateID(intactComplexGraph, "intact", "P49432")
[1] "EBI-917663"
> translateID(intactComplexGraph, "intact", NA)
         <NA>          <NA>          <NA>          <NA>          <NA> 
"EBI-1163494"  "EBI-967760" "EBI-1225105" "EBI-1225103"  "EBI-847690" 
> 
> complexSample <- complexes(intactComplexSet)[[2]]
> complexName(complexSample)
[1] "BAD:BCL-2 heterodimer"
> attributesList(complexSample)
[[1]]
curated-complex: BH3 domain-containing BAD interacts with and inhibits anti-apoptotic BCL-2. May act to prevent BCl-2 from sequestering BID and other pro-apoptotic molecules.

[[2]]
complex-synonym: BAD:BCL-2; BAD:BCL2; BCL-2:BAD; BCL2:BAD;

[[3]]
kd: 0.0

> members(complexSample)
  sourceId uniprotId multiplicity
4        4    P10415            1
8        8    Q92934            1
> 
> ## DIP: schema check failed, namespace not unique, modified
> dipxml <- file.path(xmlDir, "dip_2008_test.xml")
> dipSet <- parsePsimi25Interaction(dipxml, DIP.PSIMI25)
1 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  3% =>
  5% ==>
  8% ===>
  10% ====>
  13% =====>
  15% ======>
  18% =======>
  20% ========>
  23% =========>
  25% ==========>
  28% ===========>
  30% ============>
  33% =============>
  35% ==============>
  38% ===============>
  40% ================>
  43% =================>
  45% ==================>
  48% ===================>
  50% ====================>
  53% =====================>
  55% ======================>
  58% =======================>
  60% ========================>
  63% =========================>
  65% ==========================>
  68% ===========================>
  70% ============================>
  73% =============================>
  75% ==============================>
  78% ===============================>
  80% ================================>
  83% =================================>
  86% ==================================>
  88% ===================================>
  91% ====================================>
  93% =====================================>
  96% ======================================>
  98% =======================================>
  100% ========================================>
  Parsing interactions:
............................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................................
> dipInteractions <- interactions(dipSet)
> dipInteractionTypes <- sapply(dipInteractions, interactionType)
> stopifnot(!any(is.na(dipInteractionTypes)))
> 
> ## MatrixDB
> matrixdbxml <- file.path(xmlDir, "matrixdb_20080609.xml")
> matrixdbSet <- parsePsimi25Interaction(matrixdbxml, MATRIXDB.PSIMI25)
141 Entries found
Parsing entry 1 
  Parsing experiments: 
  Parsing interactors:

  50% ====================>
  100% ========================================>
  Parsing interactions:
.
> 
> ## MIPS: schema check failed
> ##mipsxml <- file.path(xmlDir, "mips_2007_test.xml")
> ##mipsSet <- parsePsimi25Interaction(mipsxml, MIPS.PSIMI25) ## needs implementation
> 
> ## CORUM:
> corumxml <- file.path(xmlDir,"corumPsimi")
> if(file.exists(corumxml)) {
+ corumSet <- parsePsimi25Interaction(corumxml,CORUM.PSIMI25, verbose=FALSE)
+ }
> 
> ##############################
> ## Validating PSI-MI 2.5 Files
> ##############################
> #okFile <- system.file("extdata/psi25files/intact_2008_test.xml",
> #                      package="RpsiXML")
> #errorFile <- system.file("extdata/psi25files/mips_2007_test.xml",
> #                         package="RpsiXML")
> #mif25Schema <- system.file("extdata/schemas/MIF25.xsd",package="RpsiXML")
> #stopifnot(file.exists(okFile) &&
> #          file.exists(errorFile) &&
> #          file.exists(mif25Schema))
> #
> #validatePSIMI25(okFile)
> #validatePSIMI25(errorFile)
> #validatePSIMI25(errorFile, ignore.stderr=FALSE)
> 
> 
> proc.time()
   user  system elapsed 
  19.60    0.14   20.00

name	user	system	elapsed
availableXrefs	0.47	0.00	0.47
bait	0.25	0.00	0.25
buildPCHypergraph	1.16	0.03	1.19
complexName	1.12	0.00	1.12
complexes	1.19	0.03	1.22
eListHandler	0	0	0
getAbstractByPMID	0.31	0.00	0.52
graphSpeciesConverter	1.75	0.03	1.78
interactionType	0.05	0.00	0.04
interactions	0.05	0.00	0.05
interactorInfo	0.03	0.00	0.03
interactors	0.92	0.08	1.00
null2na	0	0	0
parsePsimi25Interaction	1.17	0.00	1.17
psimi25Complex-class	0	0	0
psimi25ComplexEntry-class	0	0	0
psimi25Experiment-class	0	0	0
psimi25Graph-class	0	0	0
psimi25Hypergraph-class	0.97	0.00	0.97
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0	0	0
psimi25InteractionEntry-class	0	0	0
psimi25Interactor-class	0	0	0
psimi25Source-class	0	0	0
psimi25XML2Graph	1.59	0.00	1.59
separateXMLDataByExpt	0.33	0.00	0.33
translateID	2.50	0.01	2.52
uniprot	0	0	0
validatePSIMI25	0	0	0

name	user	system	elapsed
availableXrefs	0.43	0.00	0.42
bait	0.17	0.00	0.17
buildPCHypergraph	1.22	0.02	1.23
complexName	1.41	0.01	1.43
complexes	1.33	0.00	1.32
eListHandler	0.00	0.02	0.02
getAbstractByPMID	0.31	0.03	0.55
graphSpeciesConverter	1.95	0.06	2.01
interactionType	0.06	0.00	0.06
interactions	0.07	0.00	0.07
interactorInfo	0.03	0.00	0.03
interactors	1.28	0.08	1.36
null2na	0	0	0
parsePsimi25Interaction	1.62	0.06	1.69
psimi25Complex-class	0	0	0
psimi25ComplexEntry-class	0	0	0
psimi25Experiment-class	0	0	0
psimi25Graph-class	0.02	0.00	0.02
psimi25Hypergraph-class	1.39	0.02	1.40
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0	0	0
psimi25InteractionEntry-class	0	0	0
psimi25Interactor-class	0	0	0
psimi25Source-class	0	0	0
psimi25XML2Graph	2.47	0.01	2.49
separateXMLDataByExpt	0.37	0.02	0.39
translateID	3.08	0.03	3.11
uniprot	0	0	0
validatePSIMI25	0	0	0

CHECK report for RpsiXML on tokay1

Summary

Command output

Installation output

Tests output

Example timings