BioC 3.1: CHECK report for RpsiXML on morelia

Package: RpsiXML

Version: 2.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RpsiXML_2.10.0.tar.gz

StartedAt: 2015-10-09 05:53:38 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 05:55:57 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 138.6 seconds

RetCode: 0

Status:  OK

CheckDir: RpsiXML.Rcheck

Warnings: 0

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings RpsiXML_2.10.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-bioc/meat/RpsiXML.Rcheck’
* using R version 3.2.2 (2015-08-14)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.10.0’
* 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 ... [9s/9s] OK
* checking installed package size ... NOTE
  installed size is 33.7Mb
  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 ... OK
* 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
getAbstractByPMID: no visible global function definition for ‘pubmed’
getAbstractByPMID: no visible global function definition for
  ‘buildPubMedAbst’
hyperGraphConverter: no visible global function definition for
  ‘inciMat’
list2Matrix: no visible global function definition for ‘listLen’
list2Matrix: no visible global function definition for ‘inciMat’
psimi25Hypergraph2GraphNEL: no visible global function definition for
  ‘toGraphNEL’
removeHypergraphNAnode: no visible global function definition for
  ‘hyperedges’
separateXMLDataByExpt : <anonymous>: no visible global function
  definition for ‘listLen’
edgeLabel,psimi25Hypergraph : .local: no visible global function
  definition for ‘hyperedgeLabels’
head,missing : .local: no visible binding for global variable ‘.Object’
hyperedgeNodes,Hypergraph : .local: no visible global function
  definition for ‘hyperedges’
hyperedgeNodes,Hypergraph : .local: no visible global function
  definition for ‘hyperedgeLabels’
numEdges,psimi25Hypergraph: no visible global function definition for
  ‘hyperedges’
tail,missing : .local: no visible binding for global variable ‘.Object’
translateID,psimi25Graph : .local: no visible global function
  definition for ‘combineNodes’
translateID,psimi25Graph : .local: no visible global function
  definition for ‘nodes<-’
* 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 ... [28s/28s] OK
Examples with CPU or elapsed time > 5s
             user system elapsed
translateID 4.901  0.178   5.079
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
  Running ‘psimi25Source_test.R’ [27s/27s]
 [27s/27s] 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: 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.

* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (RpsiXML)

name	user	system	elapsed
availableXrefs	0.156	0.002	0.158
bait	0.039	0.003	0.042
buildPCHypergraph	1.484	0.024	1.509
complexName	1.462	0.009	1.470
complexes	1.843	0.179	2.022
eListHandler	0.01	0.00	0.01
getAbstractByPMID	0.348	0.009	0.763
graphSpeciesConverter	2.807	0.563	3.537
interactionType	0.079	0.001	0.080
interactions	0.079	0.003	0.081
interactorInfo	0.087	0.014	0.100
interactors	2.251	0.162	2.415
null2na	0.001	0.001	0.001
parsePsimi25Interaction	2.608	0.253	2.861
psimi25Complex-class	0.002	0.000	0.002
psimi25ComplexEntry-class	0.001	0.000	0.002
psimi25Experiment-class	0.001	0.000	0.002
psimi25Graph-class	0.002	0.000	0.002
psimi25Hypergraph-class	1.618	0.014	1.632
psimi25Hypergraph2GraphNEL	0	0	0
psimi25Interaction-class	0.001	0.000	0.001
psimi25InteractionEntry-class	0.001	0.000	0.002
psimi25Interactor-class	0.001	0.000	0.001
psimi25Source-class	0.001	0.000	0.000
psimi25XML2Graph	2.206	0.010	2.216
separateXMLDataByExpt	0.400	0.005	0.405
translateID	4.901	0.178	5.079
uniprot	0	0	0
validatePSIMI25	0.146	0.046	0.246