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Package 120/609HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.16.0
Christoph Bernau
Snapshot Date: 2013-03-24 16:21:20 -0700 (Sun, 24 Mar 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_11/madman/Rpacks/CMA
Last Changed Rev: 70050 / Revision: 74773
Last Changed Date: 2012-10-01 15:16:24 -0700 (Mon, 01 Oct 2012)
lamb1 Linux (openSUSE 12.1) / x86_64  OK  OK 
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
perceval Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: CMA
Version: 1.16.0
Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch CMA_1.16.0.tar.gz
StartedAt: 2013-03-24 23:04:15 -0700 (Sun, 24 Mar 2013)
EndedAt: 2013-03-24 23:05:54 -0700 (Sun, 24 Mar 2013)
EllapsedTime: 99.4 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/CMA.Rcheck'
* using R version 2.15.3 (2013-03-01)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'CMA/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'CMA' version '1.16.0'
* 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 whether package 'CMA' can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... 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 for unstated dependencies in R code ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
ROCinternal: no visible binding for global variable 'xlab'
ROCinternal: no visible binding for global variable 'ylab'
ROCinternal: no visible binding for global variable 'main'
ROCinternal: no visible binding for global variable 'lwd'
rfe: no visible binding for global variable 'cost'
boxplot,evaloutput: no visible binding for global variable 'main'
compare,list: no visible binding for global variable 'main'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'n.minobsinnode'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'bag.fraction'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'n.trees'
gbmCMA,matrix-numeric-missing: no visible binding for global variable
  'verbose'
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  'size'
nnetCMA,matrix-numeric-missing: no visible binding for global variable
  'MaxNWts'
prediction,data.frame-missing-data.frame-formula: no visible global
  function definition for 'predicition'
svmCMA,matrix-numeric-missing: no visible binding for global variable
  'cost'
* 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' ... NOTE
The following files should probably not be installed:
  'preamble.tex'

Consider the use of a .Rinstignore file: see 'Writing R Extensions',
or move the vignette sources from 'inst/doc' to 'vignettes'.
* checking examples ... 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 vignettes ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/CMA.Rcheck/00check.log'
for details.

CMA.Rcheck/00install.out:

* installing *source* package 'CMA' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'CMA_vignette.rnw' 
** testing if installed package can be loaded

* DONE (CMA)

CMA.Rcheck/CMA-Ex.timings:

nameusersystemelapsed
ElasticNetCMA4.1900.2724.755
GeneSelection0.3400.0720.445
GenerateLearningsets0.0160.0010.015
LassoCMA0.6180.1120.845
Planarplot0.2460.0400.327
classification0.0000.0000.001
compBoostCMA1.8360.5933.101
compare0.0000.0000.001
dldaCMA0.2540.0480.326
evaluation0.1800.0130.199
fdaCMA0.1370.0170.206
flexdaCMA0.2670.0470.379
gbmCMA4.1030.0774.283
golub0.0420.0040.045
khan0.0610.0050.067
knnCMA0.2710.0270.312
ldaCMA0.1560.0140.246
nnetCMA0.1090.0150.140
pknnCMA0.1680.0170.200
plrCMA0.6570.0530.824
pls_ldaCMA0.2180.0440.299
pls_lrCMA0.1890.0350.275
pls_rfCMA0.0900.0060.115
pnnCMA0.0520.0050.072
prediction000
qdaCMA0.1620.0170.211
rfCMA0.1160.0080.144
scdaCMA0.1430.0280.208
shrinkldaCMA0.1660.0230.228
svmCMA0.9530.0701.129
tune000