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Package 124/631HostnameOS / ArchBUILDCHECKBUILD BIN
CMA 1.17.1
Christoph Bernau
Snapshot Date: 2013-01-15 17:01:14 -0800 (Tue, 15 Jan 2013)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/CMA
Last Changed Rev: 71698 / Revision: 72575
Last Changed Date: 2012-12-06 09:33:26 -0800 (Thu, 06 Dec 2012)
george2 Linux (Ubuntu 12.04.1 LTS) / x86_64  OK  OK 
lamb2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato2 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
petty Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: CMA
Version: 1.17.1
Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings CMA_1.17.1.tar.gz
StartedAt: 2013-01-16 01:40:47 -0800 (Wed, 16 Jan 2013)
EndedAt: 2013-01-16 01:42:16 -0800 (Wed, 16 Jan 2013)
EllapsedTime: 89.0 seconds
RetCode: 0
Status:  OK 
CheckDir: CMA.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/CMA.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘CMA/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘CMA’ version ‘1.17.1’
* 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 for sufficient/correct file permissions ... OK
* checking whether package ‘CMA’ can be installed ... OK
* checking installed package size ... OK
* checking package 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 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 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
  ‘/loc/home/biocbuild/bbs-2.12-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
ElasticNetCMA4.8080.0844.895
GeneSelection0.4120.0040.418
GenerateLearningsets0.0280.0000.028
LassoCMA0.6160.0240.644
Planarplot0.2160.0120.228
classification0.0080.0040.012
compBoostCMA1.4280.0041.431
compare0.0080.0000.009
dldaCMA0.2080.0120.222
evaluation0.1680.0040.172
fdaCMA0.1120.0080.122
flexdaCMA0.2440.0040.250
gbmCMA3.1840.0443.230
golub0.0440.0000.042
khan0.0520.0000.053
knnCMA0.2440.0280.275
ldaCMA0.1560.0120.168
nnetCMA0.1080.0080.117
pknnCMA0.1760.0000.177
plrCMA1.0040.0081.012
pls_ldaCMA0.1720.0160.188
pls_lrCMA0.1560.0080.169
pls_rfCMA0.0920.0000.091
pnnCMA0.0560.0000.057
prediction0.0120.0000.012
qdaCMA0.1320.0120.147
rfCMA0.3570.0000.356
scdaCMA0.1200.0080.129
shrinkldaCMA0.1480.0080.158
svmCMA0.7360.0200.759
tune0.0120.0000.012