Package: genefu

Version: 1.4.0

Command: /Library/Frameworks/R.framework/Versions/2.14/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.4.0.tar.gz

StartedAt: 2012-03-24 01:12:32 -0700 (Sat, 24 Mar 2012)

EndedAt: 2012-03-24 01:14:34 -0700 (Sat, 24 Mar 2012)

EllapsedTime: 122.2 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.9-bioc/meat/genefu.Rcheck'
* using R version 2.14.2 (2012-02-29)
* 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 '1.4.0'
* 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 sizes of PDF files under 'inst/doc' ... OK
* 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

* 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)

name	user	system	elapsed
bimod	0.534	0.045	0.591
boxplotplus2	0.023	0.002	0.026
compare.proto.cor	1.212	0.115	1.367
compute.pairw.cor.meta	2.245	0.121	2.402
compute.proto.cor.meta	0.891	0.101	0.997
cordiff.dep	0.057	0.008	0.066
expos	0.002	0.001	0.003
fuzzy.ttest	0.002	0.000	0.002
gene70	0.372	0.030	0.405
gene76	0.092	0.008	0.102
geneid.map	0.183	0.023	0.210
genius	0.613	0.067	0.684
ggi	0.161	0.023	0.226
intrinsic.cluster	0.546	0.030	0.581
intrinsic.cluster.predict	0.460	0.028	0.494
map.datasets	0.739	0.105	0.852
mod1	0.002	0.000	0.003
mod2	0.002	0.000	0.002
nkis	0.002	0.000	0.003
npi	0.006	0.003	0.010
oncotypedx	0.169	0.018	0.188
pam50	0.029	0.003	0.031
pik3cags	0.230	0.024	0.258
ps.cluster	1.127	0.037	1.158
read.m.file	0.066	0.003	0.071
rename.duplicate	0.002	0.000	0.003
rescale	0.082	0.013	0.095
scmgene.robust	0.008	0.001	0.008
scmod1.robust	0.008	0.001	0.009
scmod2.robust	0.008	0.001	0.010
sig.gene70	0.007	0.001	0.008
sig.gene76	0.008	0.001	0.009
sig.genius	0.017	0.010	0.028
sig.ggi	0.008	0.001	0.010
sig.oncotypedx	0.005	0.001	0.006
sig.pik3cags	0.004	0.001	0.005
sig.score	0.155	0.020	0.174
sig.tamr13	0.004	0.004	0.008
ssp2003	0.046	0.005	0.051
ssp2006	0.034	0.003	0.038
st.gallen	0.011	0.005	0.043
stab.fs	0.397	0.021	0.429
stab.fs.ranking	2.452	0.029	2.487
strescR	0.002	0.000	0.002
subtype.cluster	1.095	0.102	1.211
subtype.cluster.predict	0.311	0.041	0.354
tamr13	0.106	0.011	0.121
tbrm	0.000	0.000	0.001
vdxs	0.002	0.001	0.003
weighted.meanvar	0	0	0
write.m.file	0.002	0.001	0.002