BioC 2.11: CHECK report for genefu on perceval

Package: genefu

Version: 1.8.0

Command: /Library/Frameworks/R.framework/Versions/2.15/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.8.0.tar.gz

StartedAt: 2013-03-24 23:36:23 -0700 (Sun, 24 Mar 2013)

EndedAt: 2013-03-24 23:38:11 -0700 (Sun, 24 Mar 2013)

EllapsedTime: 107.4 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 2.15.3 (2013-03-01)
* 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 '1.8.0'
* 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  5.9Mb
  sub-directories of 1Mb or more:
    data   5.0Mb
* 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 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(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 3 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	0.556	0.049	0.620
boxplotplus2	0.012	0.002	0.016
compare.proto.cor	0.881	0.113	1.024
compute.pairw.cor.meta	1.741	0.110	1.913
compute.proto.cor.meta	0.717	0.101	0.848
cordiff.dep	0.028	0.007	0.039
expos	0.002	0.001	0.006
fuzzy.ttest	0.013	0.003	0.022
gene70	0.314	0.030	0.362
gene76	0.064	0.008	0.074
geneid.map	0.218	0.022	0.247
genius	0.365	0.056	0.444
ggi	0.120	0.021	0.149
intrinsic.cluster	0.461	0.033	0.500
intrinsic.cluster.predict	0.267	0.019	0.296
map.datasets	0.658	0.110	0.810
mod1	0.001	0.001	0.002
mod2	0.002	0.001	0.003
modelOvcAngioganic	0.002	0.001	0.003
nkis	0.001	0.001	0.003
npi	0.005	0.003	0.008
oncotypedx	0.117	0.019	0.145
ovcAngiogenic	0.154	0.026	0.202
ovcCrijns	0.264	0.030	0.304
ovcTCGA	0.338	0.028	0.378
ovcYoshihara	0.102	0.026	0.137
pam50	0.022	0.003	0.027
pik3cags	0.217	0.023	0.252
ps.cluster	0.830	0.041	0.908
read.m.file	0.050	0.005	0.060
rename.duplicate	0.002	0.000	0.003
rescale	0.049	0.014	0.070
scmgene.robust	0.013	0.002	0.015
scmod1.robust	0.006	0.001	0.008
scmod2.robust	0.007	0.001	0.008
sig.gene70	0.006	0.001	0.008
sig.gene76	0.006	0.001	0.008
sig.genius	0.015	0.008	0.025
sig.ggi	0.007	0.002	0.009
sig.oncotypedx	0.005	0.001	0.005
sig.pik3cags	0.003	0.000	0.004
sig.score	0.120	0.021	0.146
sig.tamr13	0.004	0.003	0.008
sigAngiogenic	0.007	0.002	0.008
sigOvcAngiogenic	0.006	0.001	0.008
sigOvcCrijns	0.007	0.001	0.009
sigOvcSpentzos	0.008	0.002	0.009
sigOvcTCGA	0.008	0.001	0.010
sigOvcYoshihara	0.007	0.001	0.008
ssp2003	0.025	0.004	0.029
ssp2006	0.024	0.003	0.027
st.gallen	0.016	0.005	0.047
stab.fs	0.293	0.019	0.315
stab.fs.ranking	1.841	0.038	1.924
strescR	0.001	0.000	0.001
subtype.cluster	0.955	0.111	1.123
subtype.cluster.predict	0.237	0.041	0.288
tamr13	0.081	0.012	0.098
tbrm	0.001	0.000	0.000
vdxs	0.002	0.001	0.002
weighted.meanvar	0	0	0
write.m.file	0.001	0.000	0.003

Summary

Command output