BioC 3.3: CHECK report for MEAL on windows2.bioconductor.org
This page was generated on 2015-10-27 12:16:14 -0400 (Tue, 27 Oct 2015).
MEAL 1.0.1 Carlos Ruiz
Snapshot Date: 2015-10-26 20:20:04 -0400 (Mon, 26 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MEAL | Last Changed Rev: 109792 / Revision: 109948 | Last Changed Date: 2015-10-20 09:25:19 -0400 (Tue, 20 Oct 2015) |
| linux2.bioconductor.org | Linux (Ubuntu 14.04.2 LTS) / x86_64 | NotNeeded | OK | OK | |  |
windows2.bioconductor.org | Windows Server 2012 R2 Enterprise SP1 (64-bit) / x64 | 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-3.3-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-3.3-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 03:52:44 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 04:02:11 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 567.3 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-3.3-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-3.3-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-3.3-bioc/meat/MEAL.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 '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'
Undefined global functions or variables:
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' ... [77s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 13.25 1.17 14.42
plotRegion-methods 9.17 0.52 9.69
plotRDA-methods 7.54 0.65 8.20
add.methy-methods 5.75 0.72 6.47
DARegionAnalysis 5.75 0.31 6.07
** running examples for arch 'x64' ... [88s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
DAPipeline 15.14 0.77 15.90
plotRegion-methods 10.18 0.51 10.70
plotRDA-methods 8.50 0.52 9.01
add.methy-methods 8.06 0.41 8.47
DARegionAnalysis 8.21 0.21 8.43
* checking for unstated dependencies in 'tests' ... OK
* checking tests ...
** running tests for arch 'i386' ...
Running 'testthat.R' [58s]
[58s] 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-3.3-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 | 13.25 | 1.17 | 14.42 |
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DAProbe | 0.46 | 0.08 | 0.53 |
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DARegion | 1.55 | 0.20 | 1.75 |
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DARegionAnalysis | 5.75 | 0.31 | 6.07 |
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MethylationSet-class | 0 | 0 | 0 |
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RDAset | 0.97 | 0.08 | 1.05 |
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add.genexp-methods | 0.04 | 0.00 | 0.05 |
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add.methy-methods | 5.75 | 0.72 | 6.47 |
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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 | 1.31 | 0.03 | 1.36 |
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checkSamples-methods | 0.99 | 0.02 | 1.00 |
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chrNumToChar | 0 | 0 | 0 |
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createRanges | 0.02 | 0.00 | 0.02 |
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explainedVariance | 0.01 | 0.00 | 0.01 |
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exportResults-methods | 1.64 | 0.11 | 1.75 |
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filterSet-methods | 1.1 | 0.0 | 1.1 |
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getGeneVals-methods | 1.55 | 0.09 | 1.64 |
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getMs-methods | 0.86 | 0.02 | 0.88 |
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normalSNP | 0 | 0 | 0 |
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plotBestFeatures | 1.97 | 0.14 | 2.11 |
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plotEWAS-methods | 2.29 | 0.11 | 2.39 |
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plotFeature | 1.44 | 0.03 | 1.47 |
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plotQQ-methods | 2.14 | 0.19 | 2.33 |
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plotRDA-methods | 7.54 | 0.65 | 8.20 |
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plotRegion-methods | 9.17 | 0.52 | 9.69 |
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plotVolcano-methods | 2.17 | 0.33 | 2.50 |
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prepareMethylationSet | 1.28 | 0.09 | 1.37 |
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preparePhenotype | 0 | 0 | 0 |
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MEAL.Rcheck/examples_x64/MEAL-Ex.timings:
name | user | system | elapsed
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AnalysisRegionResults-class | 0.02 | 0.00 | 0.02 |
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AnalysisResults-class | 0 | 0 | 0 |
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DAPipeline | 15.14 | 0.77 | 15.90 |
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DAProbe | 0.39 | 0.02 | 0.41 |
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DARegion | 2.08 | 0.11 | 2.19 |
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DARegionAnalysis | 8.21 | 0.21 | 8.43 |
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MethylationSet-class | 0 | 0 | 0 |
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RDAset | 1.42 | 0.11 | 1.53 |
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add.genexp-methods | 0.09 | 0.00 | 0.10 |
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add.methy-methods | 8.06 | 0.41 | 8.47 |
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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 | 1.3 | 0.0 | 1.3 |
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checkSamples-methods | 1.89 | 0.05 | 1.93 |
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chrNumToChar | 0 | 0 | 0 |
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createRanges | 0.03 | 0.00 | 0.03 |
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explainedVariance | 0.03 | 0.01 | 0.05 |
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exportResults-methods | 1.80 | 0.11 | 1.90 |
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filterSet-methods | 1.33 | 0.02 | 1.34 |
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getGeneVals-methods | 2.93 | 0.20 | 3.14 |
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getMs-methods | 1.12 | 0.00 | 1.13 |
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normalSNP | 0 | 0 | 0 |
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plotBestFeatures | 1.58 | 0.06 | 1.64 |
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plotEWAS-methods | 1.72 | 0.11 | 1.83 |
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plotFeature | 1.36 | 0.06 | 1.42 |
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plotQQ-methods | 1.32 | 0.08 | 1.39 |
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plotRDA-methods | 8.50 | 0.52 | 9.01 |
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plotRegion-methods | 10.18 | 0.51 | 10.70 |
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plotVolcano-methods | 1.23 | 0.16 | 1.39 |
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prepareMethylationSet | 1.52 | 0.14 | 1.65 |
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preparePhenotype | 0 | 0 | 0 |
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