##############################################################################
##############################################################################
###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD check --install=check:RpsiXML.install-out.txt --library=/home/biocbuild/bbs-3.11-bioc/R/library --no-vignettes --timings RpsiXML_2.30.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/home/biocbuild/bbs-3.11-bioc/meat/RpsiXML.Rcheck’
* using R version 4.0.3 (2020-10-10)
* 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 ‘2.30.0’
* 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 33.5Mb
  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 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-3.11-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.

##############################################################################
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###
### Running command:
###
###   /home/biocbuild/bbs-3.11-bioc/R/bin/R CMD INSTALL RpsiXML
###
##############################################################################
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* installing to library ‘/home/biocbuild/bbs-3.11-bioc/R/library’
* installing *source* package ‘RpsiXML’ ...
** using staged installation
** 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 from temporary location
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’
** testing if installed package can be loaded from final location
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’
** testing if installed package keeps a record of temporary installation path
* DONE (RpsiXML)

R version 4.0.3 (2020-10-10) -- "Bunny-Wunnies Freak Out"
Copyright (C) 2020 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (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, 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, 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% ====================>
  56% ======================>
  62% =========================>
  69% ============================>
  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% =========>
  26% ==========>
  29% ============>
  32% =============>
  35% ==============>
  39% ================>
  42% =================>
  45% ==================>
  48% ===================>
  52% =====================>
  55% ======================>
  58% =======================>
  61% ========================>
  65% ==========================>
  68% ===========================>
  71% ============================>
  74% ==============================>
  77% ===============================>
  81% ================================>
  84% ==================================>
  87% ===================================>
  90% ====================================>
  94% ======================================>
  97% =======================================>
  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% ================>
  42% =================>
  45% ==================>
  48% ===================>
  52% =====================>
  55% ======================>
  58% =======================>
  61% ========================>
  65% ==========================>
  68% ===========================>
  71% ============================>
  74% ==============================>
  77% ===============================>
  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 
 18.710   0.279  18.997