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Package 192/514HostnameOS / ArchBUILDCHECKBUILD BIN
genefu 1.4.0
Benjamin Haibe-Kains , Markus Schroeder
Snapshot Date: 2012-03-23 18:21:46 -0700 (Fri, 23 Mar 2012)
URL: https://hedgehog.fhcrc.org/bioconductor/branches/RELEASE_2_9/madman/Rpacks/genefu
Last Changed Rev: 59920 / Revision: 64395
Last Changed Date: 2011-10-31 15:59:03 -0700 (Mon, 31 Oct 2011)
wilson2 Linux (openSUSE 11.4) / x86_64  OK [ OK ]
moscato1 Windows Server 2008 R2 Enterprise SP1 (64-bit) / x64  OK  OK  OK 
pitt Mac OS X Leopard (10.5.8) / i386  OK  OK  OK 

Summary

Package: genefu
Version: 1.4.0
Command: /home/biocbuild/bbs-2.9-bioc/R/bin/R CMD check --no-vignettes --timings genefu_1.4.0.tar.gz
StartedAt: 2012-03-24 00:29:00 -0700 (Sat, 24 Mar 2012)
EndedAt: 2012-03-24 00:30:25 -0700 (Sat, 24 Mar 2012)
EllapsedTime: 84.9 seconds
RetCode: 0
Status:  OK 
CheckDir: genefu.Rcheck
Warnings: 0

Command output

* using log directory ‘/loc/home/biocbuild/bbs-2.9-bioc/meat/genefu.Rcheck’
* using R version 2.14.2 (2012-02-29)
* using platform: x86_64-unknown-linux-gnu (64-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 ‘1.4.0’
* 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 ‘genefu’ can be installed ... OK
* checking installed package size ... NOTE
  installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
* 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 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 ... 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 R CMD build --resave-data
                     old_size new_size compress
  expos.rda             2.8Mb    2.5Mb       xz
  mod1.rda               15Kb     12Kb       xz
  mod2.rda               11Kb      9Kb       xz
  nkis.rda              721Kb    485Kb       xz
  scmod1.robust.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
  vdxs.rda              1.2Mb    665Kb       xz
* checking examples ... OK
* checking for unstated dependencies in vignettes ... NOTE
‘library’ or ‘require’ calls not declared from:
  ‘Biobase’ ‘xtable’
* 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
** help
*** installing help indices
** building package indices ...
*** tangling vignette sources ...
   ‘genefu.Rnw’ 
** testing if installed package can be loaded

* DONE (genefu)

genefu.Rcheck/genefu-Ex.timings:

nameusersystemelapsed
bimod0.5120.0200.537
boxplotplus20.0080.0000.010
compare.proto.cor1.7040.0121.714
compute.pairw.cor.meta1.8680.0081.877
compute.proto.cor.meta0.9440.0040.946
cordiff.dep0.0360.0000.037
expos0.0000.0000.003
fuzzy.ttest0.0000.0000.001
gene700.4360.0000.437
gene760.0600.0000.061
geneid.map0.1600.0040.163
genius0.6120.0000.610
ggi0.1160.0000.120
intrinsic.cluster0.4200.0040.432
intrinsic.cluster.predict0.2840.0040.286
map.datasets1.1800.0081.187
mod10.0000.0040.003
mod20.0000.0040.002
nkis0.0000.0000.002
npi0.0040.0000.006
oncotypedx0.1320.0000.134
pam500.0240.0000.025
pik3cags0.2520.0080.259
ps.cluster0.7520.0040.758
read.m.file0.0560.0000.055
rename.duplicate0.0040.0000.002
rescale0.0320.0040.035
scmgene.robust0.0040.0000.006
scmod1.robust0.0080.0000.008
scmod2.robust0.0080.0000.008
sig.gene700.0080.0000.006
sig.gene760.0080.0000.008
sig.genius0.0200.0040.028
sig.ggi0.0040.0000.009
sig.oncotypedx0.0040.0000.006
sig.pik3cags0.0040.0000.006
sig.score0.1080.0080.116
sig.tamr130.0080.0000.006
ssp20030.0240.0000.025
ssp20060.0240.0000.028
st.gallen0.0120.0000.026
stab.fs0.2920.0000.290
stab.fs.ranking1.7880.0001.786
strescR0.0000.0000.001
subtype.cluster0.8400.0200.857
subtype.cluster.predict0.2320.0000.238
tamr130.0600.0080.069
tbrm0.0000.0000.001
vdxs0.0040.0000.003
weighted.meanvar000
write.m.file0.0040.0000.002