RpsiXML 2.13.0
Jitao David Zhang
| Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/RpsiXML | | Last Changed Rev: 109592 / Revision: 109948 | | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | OK | OK | [ OK ] | |  |
| windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | OK | OK | OK | OK | |
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### Running command:
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### /home/biocbuild/bbs-3.3-bioc/R/bin/R CMD check --no-vignettes --timings RpsiXML_2.13.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.3-bioc/meat/RpsiXML.Rcheck’
* using R Under development (unstable) (2015-09-09 r69333)
* 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 ‘2.13.0’
* 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 ... [7s/7s] 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: 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’
numEdges,psimi25Hypergraph: no visible global function definition for
‘hyperedges’
tail,missing: no visible binding for global variable ‘.Object’
translateID,psimi25Graph: no visible global function definition for
‘combineNodes’
translateID,psimi25Graph: no visible global function definition for
‘nodes<-’
Undefined global functions or variables:
.Object buildPubMedAbst combineNodes hyperedgeLabels hyperedges
inciMat listLen nodes<- pubmed toGraphNEL
* 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 ... [25s/25s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
translateID 5.619 0.009 5.627
* checking for unstated dependencies in ‘tests’ ... OK
* checking tests ...
Running ‘psimi25Source_test.R’ [29s/29s]
[30s/30s] 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
‘/home/biocbuild/bbs-3.3-bioc/meat/RpsiXML.Rcheck/00check.log’
for details.
* installing *source* package ‘RpsiXML’ ...
** R
** inst
** preparing package for lazy loading
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
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* DONE (RpsiXML)