BioC 3.3: CHECK report for MAIT on morelia
This page was generated on 2015-10-22 17:54:33 -0400 (Thu, 22 Oct 2015).
MAIT 1.5.0 Francesc Fernandez-Albert
Snapshot Date: 2015-10-21 20:20:05 -0400 (Wed, 21 Oct 2015) | URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/MAIT | Last Changed Rev: 109592 / Revision: 109826 | Last Changed Date: 2015-10-13 15:59:53 -0400 (Tue, 13 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 |  |
morelia | Mac OS X Mavericks (10.9.5) / x86_64 | NotNeeded | OK | [ OK ] | OK |  |
Summary
Package: MAIT |
Version: 1.5.0 |
Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.5.0.tar.gz |
StartedAt: 2015-10-22 07:51:02 -0400 (Thu, 22 Oct 2015) |
EndedAt: 2015-10-22 07:54:39 -0400 (Thu, 22 Oct 2015) |
EllapsedTime: 217.1 seconds |
RetCode: 0 |
Status: OK |
CheckDir: MAIT.Rcheck |
Warnings: 0 |
Command output
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### Running command:
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### /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings MAIT_1.5.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-3.3-bioc/meat/MAIT.Rcheck’
* using R Under development (unstable) (2015-10-08 r69496)
* using platform: x86_64-apple-darwin13.4.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘MAIT/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘MAIT’ version ‘1.5.0’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘MAIT’ can be installed ... [12s/13s] 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' 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [102s/103s] OK
Examples with CPU or elapsed time > 5s
user system elapsed
ovClassifRatio 15.835 0.123 16.009
ovClassifRatioTable 15.003 0.112 15.135
Validation 14.924 0.140 15.106
classifRatioClasses 12.948 0.116 13.099
parameters 12.511 0.142 12.669
* 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
‘/Users/biocbuild/bbs-3.3-bioc/meat/MAIT.Rcheck/00check.log’
for details.
MAIT.Rcheck/00install.out:
* installing *source* package ‘MAIT’ ...
** R
** data
** inst
** preparing package for lazy loading
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
* DONE (MAIT)
MAIT.Rcheck/MAIT-Ex.timings:
name | user | system | elapsed
|
Biotransformations | 0.708 | 0.020 | 0.761 |
|
LSDResults | 0.448 | 0.005 | 0.454 |
|
MAITbuilder | 0.018 | 0.001 | 0.019 |
|
Validation | 14.924 | 0.140 | 15.106 |
|
classNum | 0.005 | 0.003 | 0.007 |
|
classes | 0.005 | 0.002 | 0.007 |
|
classifRatioClasses | 12.948 | 0.116 | 13.099 |
|
featureID | 0.509 | 0.003 | 0.513 |
|
featureInfo | 0.439 | 0.004 | 0.444 |
|
featureSigID | 0.465 | 0.003 | 0.467 |
|
getScoresTable | 0.507 | 0.015 | 0.522 |
|
identifyMetabolites | 1.121 | 0.007 | 1.133 |
|
loadings | 1.744 | 0.029 | 1.828 |
|
metaboliteTable | 1.410 | 0.018 | 1.434 |
|
method | 0.004 | 0.002 | 0.006 |
|
model | 2.034 | 0.028 | 2.067 |
|
models | 0.654 | 0.004 | 0.659 |
|
ovClassifRatio | 15.835 | 0.123 | 16.009 |
|
ovClassifRatioTable | 15.003 | 0.112 | 15.135 |
|
parameters | 12.511 | 0.142 | 12.669 |
|
pcaLoadings | 0.522 | 0.011 | 0.535 |
|
pcaModel | 0.533 | 0.011 | 0.544 |
|
pcaScores | 0.632 | 0.012 | 0.647 |
|
peakAggregation | 0.007 | 0.001 | 0.009 |
|
peakAnnotation | 0 | 0 | 0 |
|
plotBoxplot | 0.665 | 0.024 | 0.693 |
|
plotHeatmap | 3.032 | 0.162 | 3.198 |
|
plotPCA | 0.507 | 0.011 | 0.520 |
|
plotPLS | 1.421 | 0.019 | 1.442 |
|
plsLoadings | 1.363 | 0.018 | 1.384 |
|
plsModel | 1.416 | 0.019 | 1.436 |
|
plsScores | 1.447 | 0.020 | 1.470 |
|
pvalues | 0.444 | 0.003 | 0.448 |
|
pvaluesCorrection | 0.458 | 0.002 | 0.461 |
|
rawData | 0.003 | 0.001 | 0.004 |
|
resultsPath | 0.501 | 0.003 | 0.504 |
|
sampleProcessing | 0.001 | 0.000 | 0.000 |
|
scores | 1.519 | 0.038 | 1.562 |
|
sigPeaksTable | 0.603 | 0.006 | 0.609 |
|
spectralSigFeatures | 0.445 | 0.002 | 0.447 |
|