BioC 2.13: CHECK report for geNetClassifier on moscato1
This page was generated on 2014-04-05 09:51:19 -0700 (Sat, 05 Apr 2014).
geNetClassifier 1.2.0
Sara Aibar
| Snapshot Date: 2014-04-04 16:20:29 -0700 (Fri, 04 Apr 2014) | | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_13/madman/Rpacks/geNetClassifier | | Last Changed Rev: 81642 / Revision: 88450 | | Last Changed Date: 2013-10-14 14:29:21 -0700 (Mon, 14 Oct 2013) |
| zin1 | Linux (Ubuntu 12.04.4 LTS) / x86_64 | OK | OK | |
| moscato1 | Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64 | OK | [ OK ] | OK |
| perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | OK | OK | OK |
Summary
| Package: geNetClassifier
|
| Version: 1.2.0
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| Command: rm -rf geNetClassifier.buildbin-libdir && mkdir geNetClassifier.buildbin-libdir && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=geNetClassifier.buildbin-libdir geNetClassifier_1.2.0.tar.gz >geNetClassifier-install.out 2>&1 && D:\biocbld\bbs-2.13-bioc\R\bin\R.exe CMD check --library=geNetClassifier.buildbin-libdir --install="check:geNetClassifier-install.out" --force-multiarch --no-vignettes --timings geNetClassifier_1.2.0.tar.gz && mv geNetClassifier.buildbin-libdir/* geNetClassifier.Rcheck/ && rmdir geNetClassifier.buildbin-libdir
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| StartedAt: 2014-04-05 04:07:00 -0700 (Sat, 05 Apr 2014)
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| EndedAt: 2014-04-05 04:10:11 -0700 (Sat, 05 Apr 2014)
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| EllapsedTime: 190.9 seconds
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| RetCode: 0
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| Status: OK
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| CheckDir: geNetClassifier.Rcheck
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| Warnings: 0
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Command output
* using log directory 'D:/biocbld/bbs-2.13-bioc/meat/geNetClassifier.Rcheck'
* using R version 3.0.3 (2014-03-06)
* using platform: i386-w64-mingw32 (32-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'geNetClassifier/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'geNetClassifier' version '1.2.0'
* 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 'geNetClassifier' 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
Namespace in Imports field not imported from: 'BiocGenerics'
All declared Imports should be used.
Packages in Depends field not imported from:
'EBarrays' 'methods'
These packages need to be imported from (in the NAMESPACE file)
for when this namespace is loaded but not attached.
See the information on DESCRIPTION files in the chapter 'Creating R
packages' of 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
calculateGenesRanking: no visible global function definition for
'brewer.pal'
plotErrorNumGenes: no visible global function definition for
'brewer.pal'
plotNetwork: no visible global function definition for
'graph.data.frame'
plotNetwork: no visible global function definition for 'vcount'
plotNetwork: no visible global function definition for
'layout.fruchterman.reingold'
plotNetwork: no visible global function definition for
'get.vertex.attribute'
plotNetwork: no visible global function definition for
'get.edge.attribute'
plotNetwork: no visible global function definition for 'ecount'
plotNetwork: no visible global function definition for 'tkplot'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [40s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot.GeNetClassifierReturn 8.92 0.25 9.19
plotNetwork 5.22 0.11 5.36
** running examples for arch 'x64' ... [44s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
plot.GeNetClassifierReturn 9.12 0.29 10.39
plotNetwork 5.07 0.19 5.26
* checking for unstated dependencies in tests ... OK
* checking tests ...
** running tests for arch 'i386'
Running 'runTests.R' [2s]
[4s] OK
** running tests for arch 'x64'
Running 'runTests.R' [2s]
[4s] 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
NOTE: There were 2 notes.
See
'D:/biocbld/bbs-2.13-bioc/meat/geNetClassifier.Rcheck/00check.log'
for details.
geNetClassifier.Rcheck/00install.out:
install for i386
* installing *source* package 'geNetClassifier' ...
** 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 'geNetClassifier' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'geNetClassifier' as geNetClassifier_1.2.0.zip
* DONE (geNetClassifier)
geNetClassifier.Rcheck/examples_i386/geNetClassifier-Ex.timings:
| name | user | system | elapsed
|
| GeNetClassifierReturn-class | 1.30 | 0.01 | 2.70 |
|
| GeneralizationError-class | 0.74 | 0.00 | 0.74 |
|
| GenesNetwork-class | 1.54 | 0.36 | 1.90 |
|
| GenesRanking-class | 0.81 | 0.02 | 0.83 |
|
| calculateGenesRanking | 0.67 | 0.01 | 0.70 |
|
| externalValidation.probMatrix | 1.11 | 0.00 | 1.10 |
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| externalValidation.stats | 0.92 | 0.00 | 1.63 |
|
| gClasses-methods | 0.33 | 0.02 | 0.34 |
|
| geNetClassifier | 0.16 | 0.04 | 0.20 |
|
| genesDetails-methods | 0.45 | 0.04 | 0.48 |
|
| getEdges-methods | 0.33 | 0.01 | 0.34 |
|
| getNodes-methods | 0.35 | 0.00 | 0.36 |
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| getNumEdges-methods | 0.32 | 0.02 | 0.33 |
|
| getNumNodes-methods | 0.36 | 0.00 | 0.36 |
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| getRanking-methods | 0.46 | 0.00 | 0.47 |
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| getSubNetwork-methods | 0.36 | 0.00 | 0.36 |
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| getTopRanking-methods | 0.35 | 0.00 | 0.34 |
|
| leukemiasClassifier | 0.41 | 0.00 | 0.41 |
|
| network2txt | 1.01 | 0.00 | 1.17 |
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| numGenes-methods | 0.31 | 0.03 | 0.34 |
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| numSignificantGenes-methods | 0.35 | 0.00 | 0.35 |
|
| overview-methods | 0.53 | 0.01 | 0.54 |
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| plot.GeNetClassifierReturn | 8.92 | 0.25 | 9.19 |
|
| plot.GenesRanking | 0.37 | 0.00 | 0.50 |
|
| plotAssignments | 1.02 | 0.00 | 1.01 |
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| plotDiscriminantPower | 0.90 | 0.02 | 1.30 |
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| plotExpressionProfiles | 2.84 | 0.03 | 2.87 |
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| plotNetwork | 5.22 | 0.11 | 5.36 |
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| queryGeNetClassifier | 1.04 | 0.03 | 1.08 |
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| querySummary | 0.75 | 0.00 | 0.75 |
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geNetClassifier.Rcheck/examples_x64/geNetClassifier-Ex.timings:
| name | user | system | elapsed
|
| GeNetClassifierReturn-class | 1.54 | 0.05 | 1.59 |
|
| GeneralizationError-class | 0.57 | 0.00 | 0.56 |
|
| GenesNetwork-class | 1.43 | 0.21 | 1.64 |
|
| GenesRanking-class | 0.96 | 0.03 | 1.00 |
|
| calculateGenesRanking | 0.64 | 0.03 | 0.95 |
|
| externalValidation.probMatrix | 1.00 | 0.04 | 1.04 |
|
| externalValidation.stats | 0.75 | 0.02 | 0.76 |
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| gClasses-methods | 0.28 | 0.00 | 0.28 |
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| geNetClassifier | 0.28 | 0.00 | 0.30 |
|
| genesDetails-methods | 0.44 | 0.02 | 0.45 |
|
| getEdges-methods | 0.28 | 0.01 | 0.29 |
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| getNodes-methods | 0.3 | 0.0 | 0.3 |
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| getNumEdges-methods | 0.28 | 0.00 | 0.28 |
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| getNumNodes-methods | 0.30 | 0.00 | 0.29 |
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| getRanking-methods | 0.47 | 0.00 | 0.47 |
|
| getSubNetwork-methods | 0.33 | 0.02 | 0.35 |
|
| getTopRanking-methods | 0.32 | 0.00 | 0.32 |
|
| leukemiasClassifier | 0.39 | 0.00 | 0.39 |
|
| network2txt | 0.80 | 0.01 | 1.37 |
|
| numGenes-methods | 0.45 | 0.00 | 0.45 |
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| numSignificantGenes-methods | 0.45 | 0.02 | 0.47 |
|
| overview-methods | 0.52 | 0.00 | 0.51 |
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| plot.GeNetClassifierReturn | 9.12 | 0.29 | 10.39 |
|
| plot.GenesRanking | 0.33 | 0.00 | 0.32 |
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| plotAssignments | 1.07 | 0.02 | 1.42 |
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| plotDiscriminantPower | 0.92 | 0.02 | 2.14 |
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| plotExpressionProfiles | 1.87 | 0.01 | 3.49 |
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| plotNetwork | 5.07 | 0.19 | 5.26 |
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| queryGeNetClassifier | 1.28 | 0.01 | 2.51 |
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| querySummary | 0.85 | 0.02 | 0.86 |
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