ToPASeq 1.0.1
Ivana Ihnatova
| 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/ToPASeq | | Last Changed Rev: 96714 / Revision: 102249 | | Last Changed Date: 2014-11-13 00:09:28 -0800 (Thu, 13 Nov 2014) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | NotNeeded | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | OK | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | OK | OK | OK |
| oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | 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 ToPASeq_1.0.1.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/ToPASeq.Rcheck’
* using R version 3.1.3 (2015-03-09)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘ToPASeq/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘ToPASeq’ version ‘1.0.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘ToPASeq’ can be installed ... [45s/47s] 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
* 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
'library' or 'require' calls in package code:
‘DEGraph’ ‘Rgraphviz’
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
SPIA: no visible binding for global variable ‘defaultEdgeAttrs’
plotCliques: no visible global function definition for ‘layoutGraph’
plotGraphW: no visible binding for global variable ‘defaultEdgeAttrs’
plotGraphW: no visible global function definition for ‘layoutGraph’
plotGraphW: no visible global function definition for ‘renderGraph’
plotRagraph : .local: no visible binding for global variable
‘drawAgNode’
plotRagraph : .local: no visible global function definition for
‘graphLayout’
plotRagraph : .local: no visible global function definition for
‘upRight’
plotRagraph : .local: no visible global function definition for
‘boundBox’
plotRagraph : .local: no visible global function definition for
‘botLeft’
plotRagraph : .local: no visible global function definition for ‘getX’
plotRagraph : .local: no visible global function definition for ‘getY’
plotRagraph : .local: no visible global function definition for
‘AgNode’
plotRagraph : .local: no visible global function definition for
‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘getNodeRW’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘getNodeLW’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘getNodeHeight’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘labelText’
plotRagraph : .local : <anonymous>: no visible global function
definition for ‘txtLabel’
plotRagraph : .local: no visible global function definition for
‘AgEdge’
prepareSPIA2: no visible binding for global variable ‘defaultEdgeAttrs’
renderSpline: no visible global function definition for ‘bezierPoints’
runDEGraphSigned : <anonymous>: no visible binding for global variable
‘defaultEdgeAttrs’
runDEGraphSigned : <anonymous>: no visible global function definition
for ‘testOneGraph’
runSPIA: no visible binding for global variable ‘defaultEdgeAttrs’
runTopologyGSADirected: no visible binding for global variable ‘name’
* 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 ... OK
* checking data for ASCII and uncompressed saves ... OK
* checking sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [46s/48s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
Clipper 15.343 0.238 16.03
* checking for unstated dependencies in tests ... OK
* checking tests ...
Running ‘runTests.R’ [29s/30s]
[29s/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
NOTE: There were 2 notes.
See
‘/Users/biocbuild/bbs-3.0-bioc/meat/ToPASeq.Rcheck/00check.log’
for details.