Package: genefu

Version: 1.7.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.7.0.tar.gz

StartedAt: 2012-06-21 00:07:28 -0700 (Thu, 21 Jun 2012)

EndedAt: 2012-06-21 00:09:18 -0700 (Thu, 21 Jun 2012)

EllapsedTime: 109.7 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.11-bioc/meat/genefu.Rcheck'
* using R version 2.15.0 Patched (2012-04-26 r59216)
* 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 '1.7.0'
* 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 ... OK
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from '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

NOTE: There were 2 notes.
See
  '/Users/biocbuild/bbs-2.11-bioc/meat/genefu.Rcheck/00check.log'
for details.

* installing *source* package 'genefu' ...
** R
** data
**  moving datasets to lazyload DB
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
   'genefu.Rnw' 
** testing if installed package can be loaded

* DONE (genefu)

name	user	system	elapsed
bimod	0.588	0.051	0.674
boxplotplus2	0.016	0.003	0.022
compare.proto.cor	1.175	0.120	1.363
compute.pairw.cor.meta	2.066	0.118	2.297
compute.proto.cor.meta	0.832	0.105	1.034
cordiff.dep	0.025	0.006	0.032
expos	0.002	0.001	0.002
fuzzy.ttest	0.001	0.001	0.002
gene70	0.380	0.033	0.429
gene76	0.080	0.008	0.094
geneid.map	0.157	0.020	0.188
genius	0.637	0.074	0.776
ggi	0.228	0.024	0.259
intrinsic.cluster	0.525	0.029	0.581
intrinsic.cluster.predict	0.381	0.028	0.424
map.datasets	0.846	0.132	1.048
mod1	0.002	0.001	0.003
mod2	0.002	0.001	0.002
nkis	0.002	0.001	0.003
npi	0.007	0.004	0.010
oncotypedx	0.240	0.024	0.280
pam50	0.029	0.003	0.033
pik3cags	0.141	0.018	0.163
ps.cluster	1.165	0.046	1.258
read.m.file	0.069	0.007	0.078
rename.duplicate	0.003	0.001	0.005
rescale	0.078	0.016	0.101
scmgene.robust	0.008	0.001	0.009
scmod1.robust	0.009	0.001	0.011
scmod2.robust	0.009	0.001	0.011
sig.gene70	0.007	0.001	0.008
sig.gene76	0.010	0.001	0.011
sig.genius	0.020	0.011	0.032
sig.ggi	0.009	0.001	0.012
sig.oncotypedx	0.005	0.001	0.007
sig.pik3cags	0.005	0.001	0.006
sig.score	0.247	0.026	0.289
sig.tamr13	0.004	0.003	0.008
ssp2003	0.035	0.004	0.041
ssp2006	0.046	0.006	0.054
st.gallen	0.010	0.005	0.053
stab.fs	0.379	0.023	0.424
stab.fs.ranking	2.408	0.055	2.672
strescR	0.001	0.001	0.002
subtype.cluster	1.074	0.102	1.397
subtype.cluster.predict	0.323	0.042	0.393
tamr13	0.093	0.011	0.106
tbrm	0.001	0.000	0.001
vdxs	0.002	0.001	0.003
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.002	0.000	0.003