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Package 178/479HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.3.2
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2011-07-06 19:21:50 -0700 (Wed, 06 Jul 2011)
URL: https://hedgehog.fhcrc.org/bioconductor/trunk/madman/Rpacks/genefu
Last Changed Rev: 55722 / Revision: 56603
Last Changed Date: 2011-05-19 10:51:16 -0700 (Thu, 19 May 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 
moscato1 Windows Server 2008 R2 Enterprise (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK [ OK ] OK 

Summary

Package: genefu
Version: 1.3.2
Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.3.2.tar.gz
StartedAt: 2011-07-07 03:07:19 -0700 (Thu, 07 Jul 2011)
EndedAt: 2011-07-07 03:09:15 -0700 (Thu, 07 Jul 2011)
EllapsedTime: 116.3 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) (2011-06-22 r56208)
* using platform: i386-apple-darwin9.8.0 (32-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genefu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genefu' version '1.3.2'
* 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 ... NOTE
  
  Note: significantly better compression could be obtained
        by using tools::resaveRdaFiles() or R CMD build --resave-data
                     old_size new_size compress
  mod1.rda               15Kb     12Kb       xz
  mod2.rda               11Kb      9Kb       xz
  nki.rda               722Kb    486Kb       xz
  scmod1.rda             10Kb      8Kb    bzip2
  sig.genius.rda         10Kb      9Kb    bzip2
  ssp2003.rda            19Kb     17Kb       xz
  ssp2003.robust.rda     19Kb     17Kb       xz
  ssp2003.scale.rda      19Kb     17Kb       xz
  vdx.rda               1.2Mb    665Kb       xz
* 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: grid
Loading required package: rmeta
Loading required package: KernSmooth
KernSmooth 2.23 loaded
Copyright M. P. Wand 1997-2009
Loading required package: bootstrap
Loading required package: survivalROC
Loading required package: rpart
Loading required package: MASS
Loading required package: mlbench
Loading required package: class
Loading required package: nnet

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
bimod0.5060.0370.554
boxplotplus20.0120.0010.012
compare.proto.cor1.0380.1171.169
compute.pairw.cor.meta2.4530.1172.600
compute.proto.cor.meta0.8050.0960.915
cordiff.dep0.1050.0100.116
gene700.3580.0260.385
gene760.1570.0100.168
geneid.map0.1530.0170.172
genius0.6580.0610.724
ggi0.2260.0230.252
intrinsic.cluster0.6910.0280.729
intrinsic.cluster.predict0.4430.0200.466
map.datasets0.7350.1050.853
mod10.0030.0010.004
mod20.0020.0000.004
nki0.0020.0010.003
npi0.0180.0050.023
oncotypedx0.2390.0200.260
pam500.0270.0030.029
pik3cags0.2040.0190.229
ps.cluster1.3380.0451.392
read.m.file0.0710.0060.076
rename.duplicate0.0030.0010.003
rescale0.0870.0120.100
scmgene0.0060.0010.007
scmod10.0070.0010.009
scmod20.0070.0010.010
sig.gene700.0090.0020.011
sig.gene760.0120.0010.012
sig.genius0.0210.0100.033
sig.ggi0.0110.0010.013
sig.oncotypedx0.0060.0010.008
sig.pik3cags0.0070.0010.007
sig.score0.1750.0220.204
sig.tamr130.0050.0040.010
ssp20030.0340.0040.039
ssp20060.0430.0050.048
st.gallen0.0150.0070.053
stab.fs0.4950.0200.520
stab.fs.ranking2.8200.0362.874
strescR0.0020.0000.002
subtype.cluster0.9400.0691.020
subtype.cluster.predict0.4050.0440.452
tamr130.1360.0130.156
tbrm0.0000.0010.000
vdx0.0030.0010.003
weighted.meanvar0.0000.0000.001
weighted.ttest0.0020.0010.001
write.m.file0.0020.0000.004