RpsiXML 2.8.0
Jitao David Zhang
| Snapshot Date: 2015-04-09 16:20:12 -0700 (Thu, 09 Apr 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_0/madman/Rpacks/RpsiXML | | Last Changed Rev: 95439 / Revision: 102249 | | Last Changed Date: 2014-10-13 14:38:33 -0700 (Mon, 13 Oct 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | WARNINGS | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | WARNINGS | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | [ WARNINGS ] | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | OK | OK | WARNINGS | OK |
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch RpsiXML_2.8.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/RpsiXML.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘RpsiXML/DESCRIPTION’ ... OK
* this is package ‘RpsiXML’ version ‘2.8.0’
* 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 ... [19s/27s] 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 ... NOTE
Packages in Depends field not imported from:
‘annotate’ ‘AnnotationDbi’ ‘RBGL’ ‘XML’
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
complexEntry2graph : <anonymous>: no visible global function definition
for ‘Hyperedge’
genBPGraph: no visible global function definition for ‘ugraph’
genBPGraph: no visible global function definition for ‘removeSelfLoops’
getAbstractByPMID: no visible global function definition for ‘pubmed’
getAbstractByPMID: no visible global function definition for ‘xmlRoot’
getAbstractByPMID: no visible global function definition for
‘buildPubMedAbst’
getInteractionNodeSet: no visible global function definition for
‘getNodeSet’
getInteractorNodeSet: no visible global function definition for
‘getNodeSet’
getXmlExperimentNodeSet: no visible global function definition for
‘getNodeSet’
graphConverter: no visible global function definition for ‘idConverter’
hyperGraphConverter: no visible global function definition for
‘inciMat’
hyperGraphConverter: no visible global function definition for
‘idConverter’
list2Matrix: no visible global function definition for ‘listLen’
list2Matrix : <anonymous>: no visible global function definition for
‘Hyperedge’
list2Matrix: no visible global function definition for ‘inciMat’
parsePsimi25Complex: no visible global function definition for
‘xmlTreeParse’
parsePsimi25Complex: no visible global function definition for
‘xmlNamespaceDefinitions’
parsePsimi25Complex: no visible global function definition for
‘getNodeSet’
parsePsimi25Complex: no visible global function definition for ‘free’
parseXmlAttribute: no visible global function definition for
‘xmlGetAttr’
parseXmlAttribute: no visible global function definition for ‘xmlValue’
parseXmlAttributesListByPath: no visible global function definition for
‘getNodeSet’
parseXmlComplexNode: no visible global function definition for ‘xmlDoc’
parseXmlComplexNode: no visible global function definition for ‘free’
parseXmlEntryNodeSet: no visible global function definition for
‘xmlTreeParse’
parseXmlEntryNodeSet: no visible global function definition for
‘getDefaultNamespace’
parseXmlEntryNodeSet: no visible global function definition for
‘getNodeSet’
parseXmlEntryNodeSet: no visible global function definition for ‘free’
parseXmlExperimentNode: no visible global function definition for
‘xmlDoc’
parseXmlExperimentNode: no visible global function definition for
‘free’
parseXmlExperimentNodeSet: no visible binding for global variable
‘xmlGetAttr’
parseXmlInteractionNode: no visible global function definition for
‘xmlDoc’
parseXmlInteractionNode: no visible global function definition for
‘free’
parseXmlInteractorNode: no visible global function definition for
‘xmlDoc’
parseXmlInteractorNode: no visible global function definition for
‘free’
parseXmlInteractorNodeSet: no visible binding for global variable
‘xmlGetAttr’
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’
XMLattributeValueByPath: no visible global function definition for
‘xpathApply’
XMLattributeValueByPath: no visible binding for global variable
‘xmlGetAttr’
XMLvalueByPath: no visible global function definition for ‘xpathApply’
XMLvalueByPath: no visible binding for global variable ‘xmlValue’
numEdges,psimi25Hypergraph: no visible global function definition for
‘hyperedges’
* 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 ... WARNING
Found the following file(s) containing GNU extensions:
Makefile
Portable Makefiles do not use GNU extensions such as +=, :=, $(shell),
$(wildcard), ifeq ... endif. See section ‘Writing portable packages’ in
the ‘Writing R Extensions’ manual.
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [41s/42s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
translateID 7.324 0.072 7.407
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘psimi25Source_test.R’ [40s/42s]
[41s/43s] 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
WARNING: There was 1 warning.
NOTE: There were 4 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.
* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
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
* DONE (RpsiXML)