rBiopaxParser 2.16.0
Frank Kramer
| Snapshot Date: 2017-10-17 17:00:52 -0400 (Tue, 17 Oct 2017) | | URL: https://git.bioconductor.org/packages/rBiopaxParser | | Branch: RELEASE_3_5 | | Last Commit: 150e532 | | Last Changed Date: 2017-04-24 15:45:44 -0400 (Mon, 24 Apr 2017) |
| malbec2 | Linux (Ubuntu 16.04.1 LTS) / x86_64 | OK | OK | OK | |  |
| tokay2 | Windows Server 2012 R2 Standard / x64 | OK | OK | [ OK ] | OK | |
| veracruz2 | OS X 10.11.6 El Capitan / x86_64 | OK | OK | OK | OK | |
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### Running command:
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### rm -rf rBiopaxParser.buildbin-libdir rBiopaxParser.Rcheck && mkdir rBiopaxParser.buildbin-libdir rBiopaxParser.Rcheck && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=rBiopaxParser.buildbin-libdir rBiopaxParser_2.16.0.tar.gz >rBiopaxParser.Rcheck\00install.out 2>&1 && cp rBiopaxParser.Rcheck\00install.out rBiopaxParser-install.out && C:\Users\biocbuild\bbs-3.5-bioc\R\bin\R.exe CMD check --library=rBiopaxParser.buildbin-libdir --install="check:rBiopaxParser-install.out" --force-multiarch --no-vignettes --timings rBiopaxParser_2.16.0.tar.gz
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* using log directory 'C:/Users/biocbuild/bbs-3.5-bioc/meat/rBiopaxParser.Rcheck'
* using R version 3.4.2 Patched (2017-10-07 r73498)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'rBiopaxParser/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rBiopaxParser' version '2.16.0'
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 'rBiopaxParser' can be installed ... OK
* checking installed package size ... OK
* 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 ... NOTE
'library' or 'require' calls in package code:
'RBGL' 'RCurl' 'Rgraphviz' 'graph' 'igraph' 'nem'
Please use :: or requireNamespace() instead.
See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
addBiopaxInstance: no visible binding for global variable 'property'
addBiopaxInstances: no visible binding for global variable 'id'
addBiopaxInstances: no visible binding for global variable 'property'
addPropertiesToBiopaxInstance: no visible binding for global variable
'property'
colorGraphNodes: no visible global function definition for 'hcl'
createBiopax: no visible binding for global variable 'id'
createBiopax: no visible binding for global variable 'property'
getReferencedIDs: no visible binding for global variable
'property_attr'
getReferencedIDs: no visible binding for global variable 'property'
getReferencingIDs: no visible binding for global variable
'property_attr'
getReferencingIDs: no visible binding for global variable 'property'
internal_XMLInstance2DF: no visible binding for global variable 'i'
internal_XMLInstance2DF: no visible binding for global variable 'p'
internal_generateXMLfromBiopax: no visible binding for global variable
'id'
internal_getBiopaxModelAsDataFrame: no visible binding for global
variable 'property'
internal_propertyListToDF: no visible binding for global variable
'property'
layoutRegulatoryGraph: no visible global function definition for
'nodes'
listInstances: no visible binding for global variable 'property_value'
listInstances: no visible binding for global variable 'property'
pathway2AdjacancyMatrix: no visible global function definition for 'as'
pathway2Graph: no visible global function definition for 'new'
pathway2Graph: no visible global function definition for 'getClassDef'
pathway2Graph: no visible binding for global variable 'id'
pathway2Graph: no visible binding for global variable 'property'
pathway2RegulatoryGraph: no visible global function definition for
'new'
pathway2RegulatoryGraph: no visible global function definition for
'getClassDef'
pathway2RegulatoryGraph: no visible binding for global variable 'id'
pathway2RegulatoryGraph: no visible binding for global variable
'property'
plotRegulatoryGraph: no visible global function definition for 'nodes'
removeDisconnectedParts: no visible global function definition for
'removeNode'
removeNodes: no visible global function definition for 'edgeWeights'
removeNodes: no visible global function definition for 'na.omit'
removeNodes: no visible global function definition for 'removeNode'
removeNodes: no visible global function definition for 'addEdge'
removeProperties: no visible binding for global variable 'property'
selectInstances: no visible binding for global variable
'property_value'
transitiveReduction: no visible global function definition for 'as'
Undefined global functions or variables:
addEdge as edgeWeights getClassDef hcl i id na.omit new nodes p
property property_attr property_value removeNode
Consider adding
importFrom("grDevices", "hcl")
importFrom("methods", "as", "getClassDef", "new")
importFrom("stats", "na.omit")
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 contents of 'data' directory ... OK
* checking data for non-ASCII characters ... NOTE
Note: found 1 marked UTF-8 string
* checking data for ASCII and uncompressed saves ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... OK
** running examples for arch 'x64' ... OK
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'runTests.R'
OK
** running tests for arch 'x64' ...
Running 'runTests.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: 3 NOTEs
See
'C:/Users/biocbuild/bbs-3.5-bioc/meat/rBiopaxParser.Rcheck/00check.log'
for details.
install for i386
* installing *source* package 'rBiopaxParser' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
install for x64
* installing *source* package 'rBiopaxParser' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'rBiopaxParser' as rBiopaxParser_2.16.0.zip
* DONE (rBiopaxParser)