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Package 172/462HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.3.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2011-05-09 07:20:56 -0700 (Mon, 09 May 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu
Last Changed Rev: 54802 / Revision: 55359
Last Changed Date: 2011-04-13 15:36:43 -0700 (Wed, 13 Apr 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK  OK 
liverpool Windows Server 2003 R2 (32-bit) / x64  OK  OK  OK 
gewurz Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pelham Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: genefu
Version: 1.3.0
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.3.0.tar.gz
StartedAt: 2011-05-09 14:42:00 -0700 (Mon, 09 May 2011)
EndedAt: 2011-05-09 14:43:42 -0700 (Mon, 09 May 2011)
EllapsedTime: 102.0 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory ‘/Users/biocbuild/bbs-2.9-bioc/meat/genefu.Rcheck’
* using R version 2.14.0 Under development (unstable) (2011-04-24 r55634)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘1.3.0’
* checking package name space information ... OK
* checking package dependencies ... OK
* checking if this is a source package ... OK
* checking whether package ‘genefu’ 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 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 name space can be loaded with stated dependencies ... OK
* checking whether the name space 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 ... OK
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package(s) unavailable to check Rd xrefs: ‘multilevel’, ‘dplR’
* 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 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

genefu.Rcheck/00install.out:

* installing *source* package ‘genefu’ ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
Loading required package: survival
Loading required package: splines
Loading required package: ipred
Loading required package: rpart
Loading required package: MASS
Loading required package: mlbench
Loading required package: nnet
Loading required package: class
Loading required package: prodlim
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: survivalROC
Loading required package: SuppDists
Loading required package: grid
Loading required package: rmeta
Loading required package: bootstrap

Attaching package: ‘bootstrap’

The following object(s) are masked from ‘package:prodlim’:

    jackknife


by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt


Attaching package: ‘mclust’

The following object(s) are masked from ‘package:bootstrap’:

    diabetes

Loading required package: Biobase

Welcome to Bioconductor

  Vignettes contain introductory material. To view, type
  'browseVignettes()'. To cite Bioconductor, see
  'citation("Biobase")' and for packages 'citation("pkgname")'.

** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘genefu.Rnw’ 
** testing if installed package can be loaded

by using mclust, invoked on its own or through another package,
you accept the license agreement in the mclust LICENSE file
and at http://www.stat.washington.edu/mclust/license.txt


* DONE (genefu)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.5100.0350.561
boxplotplus20.0190.0010.019
compare.proto.cor0.8720.0890.960
compute.pairw.cor.meta1.6280.0941.724
compute.proto.cor.meta0.7560.0950.854
cordiff.dep0.0340.0070.040
gene700.4330.0290.462
gene760.0860.0070.094
geneid.map0.1840.0220.206
genius0.5980.0630.663
ggi0.2490.0240.274
intrinsic.cluster0.6860.0310.715
intrinsic.cluster.predict0.4520.0240.477
map.datasets0.6390.1070.755
mod10.0030.0010.005
mod20.0030.0010.004
nki0.0030.0010.004
npi0.0130.0040.017
oncotypedx0.2580.0250.282
pam500.0350.0030.037
pik3cags0.1730.0230.197
ps.cluster1.3810.0481.421
read.m.file0.0790.0050.093
rename.duplicate0.0030.0010.004
rescale0.0860.0140.131
scmgene0.0060.0010.007
scmod10.0080.0010.008
scmod20.0070.0020.008
sig.gene700.0100.0010.012
sig.gene760.0130.0020.015
sig.genius0.0810.0110.092
sig.ggi0.0130.0010.015
sig.oncotypedx0.0070.0010.008
sig.pik3cags0.0140.0020.016
sig.score0.1670.0180.185
sig.tamr130.0120.0040.016
ssp20030.0380.0030.041
ssp20060.1160.0060.122
st.gallen0.0210.0050.025
stab.fs0.4180.0180.439
stab.fs.ranking2.4980.0252.523
strescR0.0030.0000.002
subtype.cluster0.9080.0640.998
subtype.cluster.predict0.4120.0410.454
tamr130.1220.0110.133
tbrm0.0010.0000.001
vdx0.0030.0010.003
write.m.file0.0020.0010.003