BioC 3.2: CHECK report for MAIT on windows1.bioconductor.org
This page was generated on 2015-10-27 17:31:42 -0400 (Tue, 27 Oct 2015).
MAIT 1.4.0 Francesc Fernandez-Albert
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/MAIT | Last Changed Rev: 109589 / Revision: 109947 | Last Changed Date: 2015-10-13 15:36:05 -0400 (Tue, 13 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 | OK | OK | OK |  |
oaxaca | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | OK | OK |  |
Summary
Package: MAIT
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Version: 1.4.0
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Command: rm -rf MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.4.0.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.4.0.tar.gz
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StartedAt: 2015-10-27 03:08:45 -0400 (Tue, 27 Oct 2015)
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EndedAt: 2015-10-27 03:14:48 -0400 (Tue, 27 Oct 2015)
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EllapsedTime: 362.8 seconds
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RetCode: 0
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Status: OK
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CheckDir: MAIT.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 MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.4.0.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out && C:\biocbld\bbs-3.2-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.4.0.tar.gz
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* using log directory 'C:/biocbld/bbs-3.2-bioc/meat/MAIT.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 'MAIT/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'MAIT' version '1.4.0'
* 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 'MAIT' 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
'library' or 'require' call to 'rgl' in package code.
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 ... OK
* 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' ... [96s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
Validation 14.08 0.04 14.19
classifRatioClasses 13.62 0.07 13.69
ovClassifRatioTable 13.50 0.04 13.55
parameters 13.41 0.07 13.46
ovClassifRatio 13.18 0.05 13.24
** running examples for arch 'x64' ... [112s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ovClassifRatioTable 16.67 0.05 16.72
classifRatioClasses 16.58 0.05 16.62
ovClassifRatio 15.56 0.06 15.62
parameters 15.27 0.05 15.31
Validation 15.18 0.04 15.36
* 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: 1 NOTE
See
'C:/biocbld/bbs-3.2-bioc/meat/MAIT.Rcheck/00check.log'
for details.
MAIT.Rcheck/00install.out:
install for i386
* installing *source* package 'MAIT' ...
** R
** data
** inst
** preparing package for lazy loading
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
Creating a new generic function for 'scores' in package 'MAIT'
Creating a new generic function for 'loadings' in package 'MAIT'
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
install for x64
* installing *source* package 'MAIT' ...
** testing if installed package can be loaded
Note: the specification for S3 class "family" in package 'MatrixModels' seems equivalent to one from package 'lme4': not turning on duplicate class definitions for this class.
* MD5 sums
packaged installation of 'MAIT' as MAIT_1.4.0.zip
* DONE (MAIT)
MAIT.Rcheck/examples_i386/MAIT-Ex.timings:
name | user | system | elapsed
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Biotransformations | 0.70 | 0.03 | 0.74 |
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LSDResults | 0.47 | 0.00 | 0.47 |
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MAITbuilder | 0.01 | 0.02 | 0.03 |
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Validation | 14.08 | 0.04 | 14.19 |
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classNum | 0.02 | 0.00 | 0.01 |
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classes | 0 | 0 | 0 |
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classifRatioClasses | 13.62 | 0.07 | 13.69 |
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featureID | 0.45 | 0.00 | 0.45 |
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featureInfo | 0.43 | 0.00 | 0.42 |
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featureSigID | 0.45 | 0.00 | 0.46 |
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getScoresTable | 0.64 | 0.01 | 0.65 |
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identifyMetabolites | 1.33 | 0.02 | 1.35 |
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loadings | 1.45 | 0.00 | 1.50 |
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metaboliteTable | 1.02 | 0.01 | 1.03 |
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method | 0.01 | 0.00 | 0.01 |
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model | 1.52 | 0.05 | 1.57 |
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models | 0.44 | 0.00 | 0.43 |
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ovClassifRatio | 13.18 | 0.05 | 13.24 |
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ovClassifRatioTable | 13.50 | 0.04 | 13.55 |
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parameters | 13.41 | 0.07 | 13.46 |
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pcaLoadings | 0.52 | 0.00 | 0.52 |
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pcaModel | 0.49 | 0.03 | 0.51 |
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pcaScores | 0.54 | 0.00 | 0.55 |
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peakAggregation | 0.02 | 0.00 | 0.01 |
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peakAnnotation | 0 | 0 | 0 |
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plotBoxplot | 0.65 | 0.06 | 0.72 |
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plotHeatmap | 1.74 | 0.34 | 2.08 |
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plotPCA | 0.50 | 0.02 | 0.52 |
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plotPLS | 1.34 | 0.03 | 1.37 |
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plsLoadings | 1.38 | 0.02 | 1.39 |
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plsModel | 1.47 | 0.00 | 1.47 |
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plsScores | 1.49 | 0.03 | 1.51 |
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pvalues | 0.43 | 0.00 | 0.44 |
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pvaluesCorrection | 0.44 | 0.00 | 0.43 |
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rawData | 0 | 0 | 0 |
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resultsPath | 0.45 | 0.01 | 0.47 |
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sampleProcessing | 0 | 0 | 0 |
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scores | 1.81 | 0.05 | 1.88 |
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sigPeaksTable | 0.53 | 0.02 | 0.54 |
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spectralSigFeatures | 0.52 | 0.00 | 0.52 |
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MAIT.Rcheck/examples_x64/MAIT-Ex.timings:
name | user | system | elapsed
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Biotransformations | 0.84 | 0.03 | 0.87 |
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LSDResults | 0.64 | 0.00 | 0.64 |
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MAITbuilder | 0.01 | 0.00 | 0.01 |
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Validation | 15.18 | 0.04 | 15.36 |
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classNum | 0 | 0 | 0 |
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classes | 0 | 0 | 0 |
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classifRatioClasses | 16.58 | 0.05 | 16.62 |
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featureID | 0.52 | 0.00 | 0.52 |
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featureInfo | 0.51 | 0.02 | 0.53 |
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featureSigID | 0.57 | 0.00 | 0.58 |
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getScoresTable | 0.57 | 0.00 | 0.56 |
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identifyMetabolites | 1.09 | 0.00 | 1.10 |
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loadings | 1.69 | 0.03 | 1.72 |
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metaboliteTable | 1.22 | 0.01 | 1.23 |
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method | 0.01 | 0.00 | 0.02 |
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model | 2.02 | 0.05 | 2.06 |
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models | 0.5 | 0.0 | 0.5 |
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ovClassifRatio | 15.56 | 0.06 | 15.62 |
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ovClassifRatioTable | 16.67 | 0.05 | 16.72 |
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parameters | 15.27 | 0.05 | 15.31 |
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pcaLoadings | 0.58 | 0.03 | 0.61 |
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pcaModel | 0.54 | 0.00 | 0.55 |
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pcaScores | 0.53 | 0.01 | 0.55 |
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peakAggregation | 0 | 0 | 0 |
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peakAnnotation | 0 | 0 | 0 |
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plotBoxplot | 0.69 | 0.03 | 0.72 |
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plotHeatmap | 2.20 | 0.31 | 2.51 |
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plotPCA | 0.56 | 0.02 | 0.58 |
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plotPLS | 1.88 | 0.01 | 1.89 |
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plsLoadings | 1.70 | 0.00 | 1.71 |
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plsModel | 1.66 | 0.04 | 1.68 |
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plsScores | 1.63 | 0.01 | 1.64 |
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pvalues | 0.49 | 0.00 | 0.49 |
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pvaluesCorrection | 0.51 | 0.00 | 0.51 |
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rawData | 0.02 | 0.00 | 0.02 |
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resultsPath | 0.52 | 0.00 | 0.52 |
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sampleProcessing | 0 | 0 | 0 |
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scores | 1.82 | 0.05 | 1.87 |
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sigPeaksTable | 0.61 | 0.01 | 0.63 |
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spectralSigFeatures | 0.57 | 0.00 | 0.56 |
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