Package: RpsiXML

Version: 2.25.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RpsiXML_2.25.0.tar.gz

StartedAt: 2019-04-09 03:27:30 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 03:30:07 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 157.2 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

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### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings RpsiXML_2.25.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/RpsiXML.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.25.0’
* 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 33.4Mb
  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 sizes of PDF files under ‘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-3.9-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL RpsiXML
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘RpsiXML’ ...
** R
** inst
** byte-compile and prepare 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
** 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’
* DONE (RpsiXML)

R Under development (unstable) (2018-11-27 r75683) -- "Unsuffered Consequences"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (64-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, basename, cbind, colMeans, colSums, colnames,
    dirname, do.call, duplicated, eval, evalq, get, grep, grepl,
    intersect, is.unsorted, lapply, 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% ==================>
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  81% ================================>
  88% ===================================>
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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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  100% ========================================>
  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% =============>
  35% ==============>
  39% ================>
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  52% =====================>
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  58% =======================>
  61% ========================>
  65% ==========================>
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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 
 20.447   0.588  21.096 

name	user	system	elapsed
availableXrefs	0.055	0.002	0.059
bait	0.041	0.001	0.042
buildPCHypergraph	1.802	0.028	1.840
complexName	1.752	0.020	1.798
complexes	2.183	0.058	2.336
eListHandler	0.010	0.001	0.011
getAbstractByPMID	0.376	0.018	0.794
graphSpeciesConverter	2.381	0.057	2.462
interactionType	0.057	0.001	0.059
interactions	0.047	0.002	0.049
interactorInfo	0.057	0.001	0.058
interactors	2.227	0.108	2.515
null2na	0	0	0
parsePsimi25Interaction	2.120	0.020	2.161
psimi25Complex-class	0.002	0.001	0.002
psimi25ComplexEntry-class	0.001	0.000	0.001
psimi25Experiment-class	0.001	0.000	0.001
psimi25Graph-class	0.001	0.000	0.001
psimi25Hypergraph-class	1.815	0.014	1.839
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0.001	0.000	0.001
psimi25InteractionEntry-class	0.001	0.000	0.001
psimi25Interactor-class	0.001	0.000	0.001
psimi25Source-class	0.000	0.000	0.001
psimi25XML2Graph	2.328	0.024	2.366
separateXMLDataByExpt	0.413	0.013	0.429
translateID	4.502	0.091	4.629
uniprot	0.001	0.000	0.001
validatePSIMI25	0.068	0.019	0.089