BioC 3.1: CHECK report for MAIT on moscato2

Package: MAIT

Version: 1.2.1

Command: rm -rf MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.2.1.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.2.1.tar.gz

StartedAt: 2015-10-09 03:22:08 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 03:30:13 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 484.9 seconds

RetCode: 0

Status:  OK

CheckDir: MAIT.Rcheck

Warnings: 0

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### Running command:
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###   rm -rf MAIT.buildbin-libdir MAIT.Rcheck && mkdir MAIT.buildbin-libdir MAIT.Rcheck && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD INSTALL --build --merge-multiarch --library=MAIT.buildbin-libdir MAIT_1.2.1.tar.gz >MAIT.Rcheck\00install.out 2>&1 && cp MAIT.Rcheck\00install.out MAIT-install.out  && E:\biocbld\bbs-3.1-bioc\R\bin\R.exe CMD check --library=MAIT.buildbin-libdir --install="check:MAIT-install.out" --force-multiarch --no-vignettes --timings MAIT_1.2.1.tar.gz
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* using log directory 'E:/biocbld/bbs-3.1-bioc/meat/MAIT.Rcheck'
* using R version 3.2.2 (2015-08-14)
* 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 '1.2.1'
* 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 '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' ... [134s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ovClassifRatio      19.77   0.03   19.87
Validation          19.70   0.03   19.99
parameters          18.22   0.06   18.29
classifRatioClasses 17.66   0.05   18.00
ovClassifRatioTable 17.66   0.04   17.69
** running examples for arch 'x64' ... [153s] OK
Examples with CPU or elapsed time > 5s
                     user system elapsed
ovClassifRatioTable 24.67   0.06   24.77
ovClassifRatio      24.16   0.03   24.40
Validation          20.50   0.06   21.25
parameters          20.42   0.05   20.47
classifRatioClasses 20.03   0.08   20.14
* 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
  'E:/biocbld/bbs-3.1-bioc/meat/MAIT.Rcheck/00check.log'
for details.

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_1.2.1.zip
* DONE (MAIT)

name	user	system	elapsed
Biotransformations	1.02	0.01	1.08
LSDResults	0.57	0.00	0.57
MAITbuilder	0.04	0.00	0.03
Validation	19.70	0.03	19.99
classNum	0.01	0.00	0.12
classes	0.02	0.00	0.02
classifRatioClasses	17.66	0.05	18.00
featureID	0.58	0.00	0.58
featureInfo	0.68	0.00	0.68
featureSigID	0.75	0.00	0.75
getScoresTable	0.81	0.00	0.81
identifyMetabolites	1.53	0.02	1.55
loadings	1.98	0.01	2.32
metaboliteTable	1.37	0.00	1.37
method	0.02	0.00	0.02
model	1.81	0.03	1.84
models	0.60	0.00	0.61
ovClassifRatio	19.77	0.03	19.87
ovClassifRatioTable	17.66	0.04	17.69
parameters	18.22	0.06	18.29
pcaLoadings	0.98	0.03	1.01
pcaModel	1.00	0.01	1.03
pcaScores	1.03	0.04	1.06
peakAggregation	0.03	0.00	0.03
peakAnnotation	0	0	0
plotBoxplot	0.95	0.04	1.08
plotHeatmap	2.78	0.36	3.29
plotPCA	0.73	0.00	0.73
plotPLS	1.78	0.02	1.80
plsLoadings	1.94	0.03	1.96
plsModel	1.90	0.03	1.94
plsScores	2.07	0.01	2.09
pvalues	0.59	0.00	0.59
pvaluesCorrection	0.6	0.0	0.6
rawData	0	0	0
resultsPath	0.60	0.00	0.61
sampleProcessing	0	0	0
scores	2.47	0.04	2.49
sigPeaksTable	1.01	0.00	1.01
spectralSigFeatures	0.61	0.01	0.63

name	user	system	elapsed
Biotransformations	1.10	0.03	1.42
LSDResults	0.75	0.01	0.76
MAITbuilder	0.03	0.00	0.03
Validation	20.50	0.06	21.25
classNum	0.02	0.00	0.01
classes	0	0	0
classifRatioClasses	20.03	0.08	20.14
featureID	0.69	0.00	0.69
featureInfo	0.72	0.00	0.71
featureSigID	0.73	0.00	0.74
getScoresTable	0.75	0.03	0.78
identifyMetabolites	1.45	0.02	1.46
loadings	2.26	0.06	2.45
metaboliteTable	1.64	0.02	1.66
method	0.02	0.00	0.01
model	2.17	0.04	2.22
models	0.90	0.02	0.92
ovClassifRatio	24.16	0.03	24.40
ovClassifRatioTable	24.67	0.06	24.77
parameters	20.42	0.05	20.47
pcaLoadings	0.70	0.03	0.73
pcaModel	1.11	0.00	1.11
pcaScores	0.70	0.03	0.73
peakAggregation	0.00	0.02	0.02
peakAnnotation	0	0	0
plotBoxplot	0.81	0.03	0.85
plotHeatmap	2.75	0.26	3.03
plotPCA	0.68	0.05	0.73
plotPLS	1.97	0.02	1.99
plsLoadings	1.97	0.01	1.98
plsModel	1.98	0.00	1.98
plsScores	2.16	0.02	2.18
pvalues	0.69	0.00	0.68
pvaluesCorrection	0.73	0.00	0.74
rawData	0	0	0
resultsPath	0.72	0.00	0.71
sampleProcessing	0	0	0
scores	2.48	0.05	2.53
sigPeaksTable	1.04	0.00	1.04
spectralSigFeatures	0.71	0.02	0.72