BioC 2.12: CHECK report for genefu on lamb2

Package: genefu

Version: 1.9.0

Command: /home/biocbuild/bbs-2.12-bioc/R/bin/R CMD check --no-vignettes --timings genefu_1.9.0.tar.gz

StartedAt: 2013-01-16 02:44:31 -0800 (Wed, 16 Jan 2013)

EndedAt: 2013-01-16 02:46:16 -0800 (Wed, 16 Jan 2013)

EllapsedTime: 105.3 seconds

RetCode: 0

Status: OK

CheckDir: genefu.Rcheck

Warnings: 0

* using log directory ‘/loc/home/biocbuild/bbs-2.12-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2012-12-17 r61365)
* using platform: x86_64-unknown-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘genefu/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘genefu’ version ‘1.9.0’
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.0Mb
  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
Packages 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 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
  ‘/loc/home/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	0.664	0.016	0.684
boxplotplus2	0.020	0.000	0.019
compare.proto.cor	1.512	0.012	1.527
compute.pairw.cor.meta	1.996	0.016	2.017
compute.proto.cor.meta	1.180	0.008	1.188
cordiff.dep	0.184	0.004	0.188
expos	0.004	0.000	0.005
fuzzy.ttest	0.016	0.000	0.016
gene70	0.452	0.000	0.456
gene76	0.068	0.004	0.072
geneid.map	0.144	0.008	0.156
genius	0.484	0.004	0.486
ggi	0.152	0.004	0.153
intrinsic.cluster	0.356	0.004	0.362
intrinsic.cluster.predict	0.304	0.004	0.309
map.datasets	1.060	0.012	1.072
mod1	0.016	0.004	0.023
mod2	0.016	0.004	0.021
modelOvcAngioganic	0.020	0.000	0.021
nkis	0.02	0.00	0.02
npi	0.028	0.000	0.027
oncotypedx	0.324	0.008	0.338
ovcAngiogenic	0.132	0.000	0.129
ovcCrijns	0.128	0.000	0.127
ovcTCGA	0.408	0.000	0.411
ovcYoshihara	0.140	0.000	0.141
pam50	0.040	0.000	0.041
pik3cags	0.12	0.00	0.12
ps.cluster	0.980	0.004	0.983
read.m.file	0.076	0.004	0.083
rename.duplicate	0.02	0.00	0.02
rescale	0.072	0.000	0.079
scmgene.robust	0.024	0.000	0.023
scmod1.robust	0.040	0.004	0.040
scmod2.robust	0.052	0.004	0.056
sig.gene70	0.036	0.000	0.036
sig.gene76	0.024	0.000	0.023
sig.genius	0.044	0.000	0.045
sig.ggi	0.008	0.004	0.011
sig.oncotypedx	0.008	0.000	0.009
sig.pik3cags	0.012	0.000	0.010
sig.score	0.104	0.000	0.104
sig.tamr13	0.020	0.000	0.016
sigAngiogenic	0.020	0.000	0.017
sigOvcAngiogenic	0.004	0.000	0.010
sigOvcCrijns	0.020	0.000	0.017
sigOvcSpentzos	0.020	0.000	0.018
sigOvcTCGA	0.020	0.000	0.019
sigOvcYoshihara	0.020	0.000	0.024
ssp2003	0.032	0.004	0.040
ssp2006	0.028	0.004	0.039
st.gallen	0.016	0.000	0.031
stab.fs	0.260	0.000	0.257
stab.fs.ranking	1.553	0.024	1.573
strescR	0.008	0.004	0.013
subtype.cluster	0.652	0.008	0.662
subtype.cluster.predict	0.240	0.012	0.250
tamr13	0.128	0.000	0.126
tbrm	0.184	0.000	0.186
vdxs	0.008	0.000	0.011
weighted.meanvar	0.008	0.000	0.008
write.m.file	0.008	0.000	0.010

Summary

Command output