BioC 2.12: CHECK report for genefu on petty

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: 2013-10-08 22:28:18 -0700 (Tue, 08 Oct 2013)

EndedAt: 2013-10-08 22:30:54 -0700 (Tue, 08 Oct 2013)

EllapsedTime: 156.6 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 3.0.1 (2013-05-16)
* 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 ... [14s/15s] 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 ... [25s/25s] 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	0.847	0.036	0.892
boxplotplus2	0.044	0.001	0.045
compare.proto.cor	1.849	0.064	1.922
compute.pairw.cor.meta	2.618	0.075	2.711
compute.proto.cor.meta	1.212	0.047	1.267
cordiff.dep	0.048	0.009	0.057
expos	0.015	0.003	0.018
fuzzy.ttest	0.038	0.006	0.044
gene70	0.357	0.021	0.384
gene76	0.251	0.011	0.266
geneid.map	0.153	0.021	0.175
genius	0.615	0.031	0.656
ggi	0.152	0.015	0.167
intrinsic.cluster	0.591	0.036	0.631
intrinsic.cluster.predict	0.391	0.020	0.421
map.datasets	0.978	0.032	1.042
mod1	0.015	0.005	0.020
mod2	0.016	0.003	0.019
modelOvcAngioganic	0.015	0.003	0.017
nkis	0.016	0.003	0.018
npi	0.029	0.006	0.034
oncotypedx	0.177	0.014	0.194
ovcAngiogenic	0.344	0.008	0.354
ovcCrijns	0.286	0.014	0.304
ovcTCGA	0.547	0.021	0.575
ovcYoshihara	0.157	0.014	0.171
pam50	0.055	0.003	0.060
pik3cags	0.136	0.016	0.156
ps.cluster	1.260	0.033	1.291
read.m.file	0.090	0.007	0.097
rename.duplicate	0.014	0.003	0.018
rescale	0.072	0.011	0.083
scmgene.robust	0.025	0.002	0.027
scmod1.robust	0.024	0.002	0.026
scmod2.robust	0.021	0.004	0.025
sig.gene70	0.016	0.004	0.020
sig.gene76	0.020	0.004	0.024
sig.genius	0.030	0.012	0.043
sig.ggi	0.020	0.003	0.024
sig.oncotypedx	0.023	0.004	0.027
sig.pik3cags	0.016	0.002	0.018
sig.score	0.184	0.014	0.197
sig.tamr13	0.146	0.007	0.155
sigAngiogenic	0.017	0.005	0.022
sigOvcAngiogenic	0.016	0.005	0.021
sigOvcCrijns	0.016	0.004	0.021
sigOvcSpentzos	0.016	0.004	0.020
sigOvcTCGA	0.017	0.005	0.023
sigOvcYoshihara	0.017	0.005	0.022
ssp2003	0.042	0.007	0.049
ssp2006	0.041	0.008	0.050
st.gallen	0.016	0.009	0.027
stab.fs	0.431	0.014	0.449
stab.fs.ranking	2.642	0.056	2.714
strescR	0.004	0.002	0.006
subtype.cluster	0.945	0.052	1.016
subtype.cluster.predict	0.333	0.018	0.357
tamr13	0.120	0.008	0.127
tbrm	0.159	0.003	0.164
vdxs	0.007	0.005	0.012
weighted.meanvar	0.006	0.004	0.013
write.m.file	0.008	0.004	0.018