BioC 3.2: CHECK report for MEAL on windows1.bioconductor.org
This page was generated on 2015-10-27 17:32:36 -0400 (Tue, 27 Oct 2015).
MEAL 1.0.1 Carlos Ruiz
Snapshot Date: 2015-10-26 19:24:07 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_3_2/madman/Rpacks/MEAL | Last Changed Rev: 109793 / Revision: 109947 | Last Changed Date: 2015-10-20 09:42:23 -0400 (Tue, 20 Oct 2015) |
| linux1.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows1.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | NotNeeded | OK | [ OK ] | OK |  |
perceval | Mac OS X Snow Leopard (10.6.8) / x86_64 | NotNeeded | TIMEOUT | skipped | skipped | |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: MEAL
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Version: 1.0.1
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Command: rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.1.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.1.tar.gz
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StartedAt: 2015-10-27 03:17:51 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 03:27:34 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 583.5 seconds
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RetCode: 0
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Status: OK
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CheckDir: MEAL.Rcheck
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Warnings: 0
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Command output
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### Running command:
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### rm -rf MEAL.buildbin-libdir MEAL.Rcheck && mkdir MEAL.buildbin-libdir MEAL.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MEAL.buildbin-libdir MEAL_1.0.1.tar.gz >MEAL.Rcheck\00install.out 2>&1 && cp MEAL.Rcheck\00install.out MEAL-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MEAL.buildbin-libdir --install="check:MEAL-install.out" --force-multiarch --no-vignettes --timings MEAL_1.0.1.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MEAL.Rcheck'
* using R version 3.2.2 Patched (2015-08-16 r69094)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--no-vignettes'
* checking for file 'MEAL/DESCRIPTION' ... OK
* this is package 'MEAL' 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 whether package 'MEAL' 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
** checking loading without being on the library search path ... 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 loading without being on the library search path ... OK
* checking dependencies in R code ... NOTE
Unexported object imported by a ':::' call: 'S4Vectors:::selectSome'
See the note in ?`:::` about the use of this operator.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
plotVolcano,AnalysisResults: no visible binding for global variable
'adj.p'
* 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 installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... OK
* checking examples ...
** running examples for arch 'i386' ... [74s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 13.35 1.01 14.36
plotRDA-methods 7.69 0.67 8.36
plotRegion-methods 7.00 0.43 7.44
add.methy-methods 6.16 0.89 7.05
DARegionAnalysis 5.34 0.33 5.67
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 13.97 0.64 14.61
plotRegion-methods 9.69 0.38 10.06
plotRDA-methods 8.34 0.42 8.76
add.methy-methods 8.01 0.56 8.58
DARegionAnalysis 7.22 0.19 7.40
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [52s]
[53s] OK
** running tests for arch 'x64' ...
Running 'testthat.R' [62s]
[63s] 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: 2 NOTEs
See
'C:/biocbld/bbs-3.2-bioc/meat/MEAL.Rcheck/00check.log'
for details.
MEAL.Rcheck/00install.out:
install for i386
* installing *source* package 'MEAL' ...
** R
** 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 'MEAL' ...
** testing if installed package can be loaded
* MD5 sums
packaged installation of 'MEAL' as MEAL_1.0.1.zip
* DONE (MEAL)
MEAL.Rcheck/examples_i386/MEAL-Ex.timings:
name | user | system | elapsed
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AnalysisRegionResults-class | 0 | 0 | 0 |
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AnalysisResults-class | 0 | 0 | 0 |
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DAPipeline | 13.35 | 1.01 | 14.36 |
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DAProbe | 0.61 | 0.07 | 0.67 |
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DARegion | 1.53 | 0.09 | 1.62 |
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DARegionAnalysis | 5.34 | 0.33 | 5.67 |
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MethylationSet-class | 0 | 0 | 0 |
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RDAset | 1.08 | 0.04 | 1.13 |
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add.genexp-methods | 0.05 | 0.00 | 0.04 |
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add.methy-methods | 6.16 | 0.89 | 7.05 |
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add.set-methods | 0.03 | 0.00 | 0.04 |
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calculateRelevantSNPs | 0 | 0 | 0 |
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checkProbes-methods | 1.16 | 0.05 | 1.20 |
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checkSamples-methods | 1.46 | 0.06 | 1.52 |
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chrNumToChar | 0 | 0 | 0 |
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createRanges | 0.02 | 0.00 | 0.01 |
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explainedVariance | 0.01 | 0.00 | 0.02 |
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exportResults-methods | 1.04 | 0.05 | 1.08 |
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filterSet-methods | 1.26 | 0.06 | 1.32 |
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getGeneVals-methods | 1.01 | 0.07 | 1.08 |
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getMs-methods | 1.25 | 0.07 | 1.33 |
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normalSNP | 0 | 0 | 0 |
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plotBestFeatures | 1.44 | 0.02 | 1.45 |
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plotEWAS-methods | 1.82 | 0.09 | 1.93 |
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plotFeature | 1.81 | 0.08 | 1.89 |
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plotQQ-methods | 1.78 | 0.10 | 1.88 |
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plotRDA-methods | 7.69 | 0.67 | 8.36 |
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plotRegion-methods | 7.00 | 0.43 | 7.44 |
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plotVolcano-methods | 1.70 | 0.14 | 1.84 |
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prepareMethylationSet | 1.03 | 0.05 | 1.08 |
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preparePhenotype | 0.02 | 0.00 | 0.01 |
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MEAL.Rcheck/examples_x64/MEAL-Ex.timings:
name | user | system | elapsed
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AnalysisRegionResults-class | 0 | 0 | 0 |
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AnalysisResults-class | 0.02 | 0.00 | 0.02 |
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DAPipeline | 13.97 | 0.64 | 14.61 |
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DAProbe | 0.54 | 0.05 | 0.58 |
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DARegion | 2.05 | 0.12 | 2.17 |
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DARegionAnalysis | 7.22 | 0.19 | 7.40 |
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MethylationSet-class | 0 | 0 | 0 |
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RDAset | 1.32 | 0.10 | 1.41 |
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add.genexp-methods | 0.05 | 0.00 | 0.05 |
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add.methy-methods | 8.01 | 0.56 | 8.58 |
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add.set-methods | 0.05 | 0.00 | 0.04 |
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calculateRelevantSNPs | 0 | 0 | 0 |
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checkProbes-methods | 1.23 | 0.01 | 1.25 |
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checkSamples-methods | 1.28 | 0.00 | 1.28 |
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chrNumToChar | 0 | 0 | 0 |
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createRanges | 0.02 | 0.00 | 0.02 |
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explainedVariance | 0.03 | 0.00 | 0.03 |
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exportResults-methods | 1.83 | 0.08 | 2.08 |
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filterSet-methods | 1.13 | 0.03 | 1.16 |
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getGeneVals-methods | 2.60 | 0.14 | 2.74 |
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getMs-methods | 0.99 | 0.02 | 1.00 |
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normalSNP | 0 | 0 | 0 |
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plotBestFeatures | 1.72 | 0.06 | 1.78 |
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plotEWAS-methods | 2.26 | 0.17 | 2.43 |
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plotFeature | 1.98 | 0.10 | 2.08 |
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plotQQ-methods | 2.18 | 0.14 | 2.31 |
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plotRDA-methods | 8.34 | 0.42 | 8.76 |
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plotRegion-methods | 9.69 | 0.38 | 10.06 |
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plotVolcano-methods | 2.16 | 0.07 | 2.24 |
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prepareMethylationSet | 1.34 | 0.03 | 1.38 |
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preparePhenotype | 0 | 0 | 0 |
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