BioC 2.12: CHECK report for genefu on pelham

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: 2013-03-24 05:29:09 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 05:31:30 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 141.3 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 beta (2013-03-21 r62346)
* 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 '1.9.1'
* 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 ... [13s/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 installed files from 'inst/doc' ... OK
* checking examples ... [23s/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
   'genefu.Rnw' 
** testing if installed package can be loaded
* DONE (genefu)

name	user	system	elapsed
bimod	0.798	0.043	0.902
boxplotplus2	0.052	0.002	0.055
compare.proto.cor	1.943	0.068	2.240
compute.pairw.cor.meta	2.368	0.087	2.581
compute.proto.cor.meta	1.155	0.058	1.319
cordiff.dep	0.053	0.015	0.072
expos	0.016	0.004	0.021
fuzzy.ttest	0.030	0.011	0.042
gene70	0.314	0.029	0.364
gene76	0.090	0.013	0.110
geneid.map	0.154	0.017	0.180
genius	0.491	0.030	0.557
ggi	0.302	0.024	0.349
intrinsic.cluster	0.531	0.029	0.591
intrinsic.cluster.predict	0.354	0.024	0.400
map.datasets	1.091	0.054	1.203
mod1	0.014	0.004	0.017
mod2	0.015	0.003	0.020
modelOvcAngioganic	0.016	0.003	0.021
nkis	0.015	0.003	0.019
npi	0.029	0.007	0.037
oncotypedx	0.180	0.019	0.212
ovcAngiogenic	0.215	0.019	0.249
ovcCrijns	0.164	0.023	0.193
ovcTCGA	0.488	0.021	0.533
ovcYoshihara	0.181	0.022	0.211
pam50	0.040	0.008	0.050
pik3cags	0.141	0.018	0.166
ps.cluster	1.102	0.052	1.211
read.m.file	0.087	0.010	0.104
rename.duplicate	0.017	0.005	0.023
rescale	0.085	0.014	0.104
scmgene.robust	0.018	0.002	0.020
scmod1.robust	0.027	0.006	0.034
scmod2.robust	0.021	0.007	0.030
sig.gene70	0.020	0.006	0.027
sig.gene76	0.012	0.005	0.017
sig.genius	0.029	0.014	0.045
sig.ggi	0.021	0.006	0.027
sig.oncotypedx	0.019	0.006	0.026
sig.pik3cags	0.020	0.005	0.028
sig.score	0.170	0.021	0.204
sig.tamr13	0.025	0.007	0.034
sigAngiogenic	0.021	0.003	0.027
sigOvcAngiogenic	0.011	0.005	0.016
sigOvcCrijns	0.022	0.006	0.028
sigOvcSpentzos	0.020	0.005	0.028
sigOvcTCGA	0.013	0.005	0.017
sigOvcYoshihara	0.022	0.006	0.030
ssp2003	0.047	0.010	0.059
ssp2006	0.051	0.009	0.065
st.gallen	0.023	0.009	0.050
stab.fs	0.380	0.017	0.420
stab.fs.ranking	2.263	0.055	2.440
strescR	0.005	0.003	0.008
subtype.cluster	1.070	0.074	1.231
subtype.cluster.predict	0.297	0.031	0.342
tamr13	0.113	0.014	0.135
tbrm	0.020	0.004	0.026
vdxs	0.013	0.003	0.016
weighted.meanvar	0.021	0.005	0.027
write.m.file	0.014	0.003	0.018

Summary

Command output