Package: genefu

Version: 1.10.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.10.0.tar.gz

StartedAt: 2013-05-01 05:44:27 -0700 (Wed, 01 May 2013)

EndedAt: 2013-05-01 05:46:46 -0700 (Wed, 01 May 2013)

EllapsedTime: 139.2 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

* using log directory '/Users/biocbuild/bbs-2.12-bioc/meat/genefu.Rcheck'
* using R version 3.0.0 Patched (2013-04-08 r62531)
* using platform: x86_64-apple-darwin10.8.0 (64-bit)
* using session charset: ASCII
* using option '--no-vignettes'
* checking for file 'genefu/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'genefu' version '1.10.0'
* 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 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 ... [13s/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 installed files from 'inst/doc' ... OK
* checking examples ... [22s/23s] 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
** testing if installed package can be loaded
* DONE (genefu)

name	user	system	elapsed
bimod	0.743	0.038	0.811
boxplotplus2	0.039	0.001	0.043
compare.proto.cor	1.795	0.069	1.983
compute.pairw.cor.meta	2.112	0.075	2.308
compute.proto.cor.meta	1.116	0.056	1.248
cordiff.dep	0.050	0.013	0.067
expos	0.014	0.004	0.018
fuzzy.ttest	0.031	0.009	0.040
gene70	0.291	0.024	0.340
gene76	0.088	0.013	0.106
geneid.map	0.165	0.021	0.194
genius	0.574	0.042	0.621
ggi	0.119	0.020	0.139
intrinsic.cluster	0.479	0.033	0.526
intrinsic.cluster.predict	0.358	0.029	0.441
map.datasets	1.106	0.061	1.309
mod1	0.015	0.004	0.020
mod2	0.015	0.003	0.019
modelOvcAngioganic	0.016	0.004	0.022
nkis	0.015	0.003	0.019
npi	0.031	0.007	0.040
oncotypedx	0.273	0.023	0.364
ovcAngiogenic	0.132	0.021	0.162
ovcCrijns	0.140	0.021	0.170
ovcTCGA	0.488	0.022	0.539
ovcYoshihara	0.146	0.030	0.187
pam50	0.043	0.011	0.054
pik3cags	0.130	0.022	0.162
ps.cluster	1.023	0.048	1.108
read.m.file	0.078	0.018	0.268
rename.duplicate	0.017	0.005	0.024
rescale	0.070	0.017	0.093
scmgene.robust	0.023	0.005	0.027
scmod1.robust	0.024	0.005	0.029
scmod2.robust	0.024	0.005	0.030
sig.gene70	0.025	0.008	0.033
sig.gene76	0.011	0.005	0.016
sig.genius	0.021	0.016	0.037
sig.ggi	0.022	0.008	0.031
sig.oncotypedx	0.017	0.006	0.025
sig.pik3cags	0.018	0.005	0.024
sig.score	0.137	0.022	0.166
sig.tamr13	0.007	0.006	0.014
sigAngiogenic	0.020	0.006	0.027
sigOvcAngiogenic	0.012	0.004	0.019
sigOvcCrijns	0.022	0.005	0.029
sigOvcSpentzos	0.012	0.005	0.018
sigOvcTCGA	0.022	0.005	0.027
sigOvcYoshihara	0.022	0.006	0.028
ssp2003	0.056	0.011	0.067
ssp2006	0.049	0.011	0.062
st.gallen	0.025	0.012	0.058
stab.fs	0.367	0.009	0.390
stab.fs.ranking	2.214	0.047	2.377
strescR	0.005	0.003	0.008
subtype.cluster	0.963	0.071	1.096
subtype.cluster.predict	0.264	0.032	0.311
tamr13	0.082	0.010	0.097
tbrm	0.010	0.004	0.015
vdxs	0.012	0.005	0.018
weighted.meanvar	0.012	0.004	0.016
write.m.file	0.012	0.004	0.016