Package: genefu

Version: 1.9.1

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.9.1.tar.gz

StartedAt: 2013-03-25 02:35:25 -0700 (Mon, 25 Mar 2013)

EndedAt: 2013-03-25 02:37:23 -0700 (Mon, 25 Mar 2013)

EllapsedTime: 118.0 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genefu.Rcheck'
* using R Under development (unstable) (2013-02-26 r62077)
* 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 '1.9.1'
* 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 for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking whether package 'genefu' can be installed ... [14s/14s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... OK
* checking for left-over 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 ... NOTE
prepare_Rd: modelOvcAngioganic.Rd:20-21: Dropping empty section \references
prepare_Rd: sigAngiogenic.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcAngiogenic.Rd:20-22: Dropping empty section \references
prepare_Rd: sigOvcCrijns.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcSpentzos.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcTCGA.Rd:20-21: Dropping empty section \references
prepare_Rd: sigOvcYoshihara.Rd:19-20: Dropping empty section \references
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Package unavailable to check Rd xrefs: '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 ... [18s/18s] 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 3 notes.
See
  '/Users/biocbuild/bbs-2.12-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	0.488	0.045	0.536
boxplotplus2	0.015	0.007	0.022
compare.proto.cor	1.081	0.116	1.201
compute.pairw.cor.meta	1.660	0.103	1.775
compute.proto.cor.meta	0.614	0.079	0.699
cordiff.dep	0.121	0.018	0.139
expos	0.003	0.004	0.008
fuzzy.ttest	0.010	0.012	0.021
gene70	0.225	0.030	0.255
gene76	0.072	0.014	0.086
geneid.map	0.189	0.024	0.213
genius	0.362	0.044	0.408
ggi	0.107	0.019	0.126
intrinsic.cluster	0.428	0.027	0.453
intrinsic.cluster.predict	0.459	0.029	0.489
map.datasets	0.644	0.098	0.744
mod1	0.009	0.006	0.018
mod2	0.015	0.006	0.020
modelOvcAngioganic	0.010	0.007	0.016
nkis	0.009	0.006	0.016
npi	0.013	0.008	0.022
oncotypedx	0.183	0.025	0.209
ovcAngiogenic	0.198	0.025	0.224
ovcCrijns	0.104	0.023	0.127
ovcTCGA	0.372	0.028	0.401
ovcYoshihara	0.111	0.025	0.137
pam50	0.034	0.009	0.043
pik3cags	0.122	0.022	0.143
ps.cluster	1.002	0.033	1.027
read.m.file	0.084	0.017	0.101
rename.duplicate	0.019	0.008	0.027
rescale	0.134	0.023	0.156
scmgene.robust	0.008	0.005	0.014
scmod1.robust	0.011	0.007	0.018
scmod2.robust	0.011	0.007	0.017
sig.gene70	0.009	0.006	0.015
sig.gene76	0.011	0.006	0.018
sig.genius	0.017	0.012	0.029
sig.ggi	0.011	0.006	0.017
sig.oncotypedx	0.010	0.006	0.016
sig.pik3cags	0.008	0.006	0.014
sig.score	0.127	0.024	0.151
sig.tamr13	0.016	0.008	0.025
sigAngiogenic	0.020	0.007	0.027
sigOvcAngiogenic	0.017	0.006	0.026
sigOvcCrijns	0.021	0.007	0.028
sigOvcSpentzos	0.012	0.006	0.019
sigOvcTCGA	0.014	0.007	0.020
sigOvcYoshihara	0.013	0.007	0.020
ssp2003	0.037	0.011	0.046
ssp2006	0.033	0.010	0.043
st.gallen	0.018	0.014	0.059
stab.fs	0.298	0.024	0.323
stab.fs.ranking	1.756	0.038	1.797
strescR	0.007	0.005	0.013
subtype.cluster	0.779	0.075	0.862
subtype.cluster.predict	0.312	0.041	0.357
tamr13	0.090	0.015	0.106
tbrm	0.006	0.006	0.011
vdxs	0.004	0.004	0.008
weighted.meanvar	0.006	0.006	0.011
write.m.file	0.007	0.006	0.013