BioC 3.3: CHECK report for RpsiXML on windows2.bioconductor.org
This page was generated on 2015-10-27 12:14:27 -0400 (Tue, 27 Oct 2015).
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 | |
Summary
| Package: RpsiXML
|
| Version: 2.13.0
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| Command: rm -rf RpsiXML.buildbin-libdir RpsiXML.Rcheck && mkdir RpsiXML.buildbin-libdir RpsiXML.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.13.0.tar.gz >RpsiXML.Rcheck\00install.out 2>&1 && cp RpsiXML.Rcheck\00install.out RpsiXML-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.13.0.tar.gz
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| StartedAt: 2015-10-27 05:46:15 -0400 (Tue, 27 Oct 2015)
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| EndedAt: 2015-10-27 05:49:09 -0400 (Tue, 27 Oct 2015)
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| EllapsedTime: 173.7 seconds
|
| RetCode: 0
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| Status: OK
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| CheckDir: RpsiXML.Rcheck
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| Warnings: 0
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Command output
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###
### Running command:
###
### rm -rf RpsiXML.buildbin-libdir RpsiXML.Rcheck && mkdir RpsiXML.buildbin-libdir RpsiXML.Rcheck && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=RpsiXML.buildbin-libdir RpsiXML_2.13.0.tar.gz >RpsiXML.Rcheck\00install.out 2>&1 && cp RpsiXML.Rcheck\00install.out RpsiXML-install.out && c:\biocbld\bbs-3.3-bioc\R\bin\R.exe CMD check --library=RpsiXML.buildbin-libdir --install="check:RpsiXML-install.out" --force-multiarch --no-vignettes --timings RpsiXML_2.13.0.tar.gz
###
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* using log directory 'c:/biocbld/bbs-3.3-bioc/meat/RpsiXML.Rcheck'
* using R Under development (unstable) (2015-09-22 r69418)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* 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 whether package 'RpsiXML' can be installed ... 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
* loading checks for arch 'i386'
** 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
* loading checks for arch 'x64'
** 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 ...
** running examples for arch 'i386' ... [19s] OK
** running examples for arch 'x64' ... [24s] OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'psimi25Source_test.R' [21s]
[21s] OK
** running tests for arch 'x64' ...
Running 'psimi25Source_test.R' [21s]
[21s] 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
'c:/biocbld/bbs-3.3-bioc/meat/RpsiXML.Rcheck/00check.log'
for details.
RpsiXML.Rcheck/00install.out:
install for i386
* 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
install for x64
* installing *source* package 'RpsiXML' ...
** testing if installed package can be loaded
No methods found in "Biobase" for requests: listlen
No methods found in "annotate" for requests: pubmed, buildPubMedAbst
* MD5 sums
packaged installation of 'RpsiXML' as RpsiXML_2.13.0.zip
* DONE (RpsiXML)
RpsiXML.Rcheck/examples_i386/RpsiXML-Ex.timings:
| name | user | system | elapsed
|
| availableXrefs | 0.05 | 0.00 | 0.05 |
|
| bait | 0.06 | 0.00 | 0.06 |
|
| buildPCHypergraph | 1.43 | 0.01 | 1.44 |
|
| complexName | 1.18 | 0.00 | 1.19 |
|
| complexes | 1.34 | 0.03 | 1.38 |
|
| eListHandler | 0 | 0 | 0 |
|
| getAbstractByPMID | 0.37 | 0.05 | 0.52 |
|
| graphSpeciesConverter | 1.89 | 0.06 | 1.95 |
|
| interactionType | 0.03 | 0.00 | 0.03 |
|
| interactions | 0.03 | 0.02 | 0.04 |
|
| interactorInfo | 0.05 | 0.00 | 0.05 |
|
| interactors | 1.26 | 0.06 | 1.33 |
|
| null2na | 0 | 0 | 0 |
|
| parsePsimi25Interaction | 1.60 | 0.02 | 1.61 |
|
| psimi25Complex-class | 0 | 0 | 0 |
|
| psimi25ComplexEntry-class | 0 | 0 | 0 |
|
| psimi25Experiment-class | 0 | 0 | 0 |
|
| psimi25Graph-class | 0 | 0 | 0 |
|
| psimi25Hypergraph-class | 1.33 | 0.00 | 1.33 |
|
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 |
|
| psimi25Interaction-class | 0 | 0 | 0 |
|
| psimi25InteractionEntry-class | 0 | 0 | 0 |
|
| psimi25Interactor-class | 0 | 0 | 0 |
|
| psimi25Source-class | 0 | 0 | 0 |
|
| psimi25XML2Graph | 1.72 | 0.00 | 1.72 |
|
| separateXMLDataByExpt | 0.31 | 0.01 | 0.33 |
|
| translateID | 3.14 | 0.02 | 3.15 |
|
| uniprot | 0 | 0 | 0 |
|
| validatePSIMI25 | 0 | 0 | 0 |
|
RpsiXML.Rcheck/examples_x64/RpsiXML-Ex.timings:
| name | user | system | elapsed
|
| availableXrefs | 0.05 | 0.00 | 0.04 |
|
| bait | 0.06 | 0.02 | 0.08 |
|
| buildPCHypergraph | 1.71 | 0.00 | 1.70 |
|
| complexName | 1.46 | 0.00 | 1.47 |
|
| complexes | 1.72 | 0.00 | 1.72 |
|
| eListHandler | 0.02 | 0.00 | 0.02 |
|
| getAbstractByPMID | 0.44 | 0.03 | 0.62 |
|
| graphSpeciesConverter | 2.32 | 0.02 | 2.35 |
|
| interactionType | 0.05 | 0.00 | 0.05 |
|
| interactions | 0.04 | 0.00 | 0.05 |
|
| interactorInfo | 0.07 | 0.00 | 0.06 |
|
| interactors | 1.53 | 0.08 | 1.61 |
|
| null2na | 0 | 0 | 0 |
|
| parsePsimi25Interaction | 2.12 | 0.03 | 2.17 |
|
| psimi25Complex-class | 0 | 0 | 0 |
|
| psimi25ComplexEntry-class | 0 | 0 | 0 |
|
| psimi25Experiment-class | 0 | 0 | 0 |
|
| psimi25Graph-class | 0.00 | 0.01 | 0.02 |
|
| psimi25Hypergraph-class | 1.72 | 0.03 | 1.75 |
|
| psimi25Hypergraph2GraphNEL | 0 | 0 | 0 |
|
| psimi25Interaction-class | 0 | 0 | 0 |
|
| psimi25InteractionEntry-class | 0 | 0 | 0 |
|
| psimi25Interactor-class | 0 | 0 | 0 |
|
| psimi25Source-class | 0 | 0 | 0 |
|
| psimi25XML2Graph | 2.05 | 0.02 | 2.07 |
|
| separateXMLDataByExpt | 0.40 | 0.00 | 0.41 |
|
| translateID | 4.29 | 0.05 | 4.33 |
|
| uniprot | 0 | 0 | 0 |
|
| validatePSIMI25 | 0 | 0 | 0 |
|