BioC 2.14: CHECK report for genefu on zin2

Package: genefu

Version: 1.14.0

Command: /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings genefu_1.14.0.tar.gz

StartedAt: 2014-10-07 23:48:34 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:50:34 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 119.9 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-2.14-bioc/R/bin/R CMD check --no-vignettes --timings genefu_1.14.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-2.14-bioc/meat/genefu.Rcheck’
* using R version 3.1.1 (2014-07-10)
* 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 ‘1.14.0’
* 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 ... [11s/12s] 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 ‘build’ 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 dependencies in R code ... NOTE
Unexported objects imported by ':::' calls:
  ‘mclust:::grid1’ ‘mclust:::grid2’
  See the note in ?`:::` about the use of this operator.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* 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 ... OK
* 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 files in ‘vignettes’ ... OK
* checking examples ... [14s/14s] 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 vignette outputs ... SKIPPED
* checking PDF version of manual ... OK

NOTE: There were 3 notes.
See
  ‘/home/biocbuild/bbs-2.14-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	0.480	0.016	0.503
boxplotplus2	0.008	0.000	0.010
compare.proto.cor	0.760	0.008	0.776
compute.pairw.cor.meta	1.308	0.020	1.332
compute.proto.cor.meta	0.444	0.000	0.450
cordiff.dep	0.012	0.000	0.012
endoPredict	0.024	0.000	0.026
expos	0.004	0.000	0.002
fuzzy.ttest	0.004	0.000	0.003
gene70	0.168	0.000	0.169
gene76	0.044	0.000	0.045
geneid.map	0.208	0.000	0.206
genius	0.200	0.004	0.206
ggi	0.2	0.0	0.2
intrinsic.cluster	0.296	0.004	0.276
intrinsic.cluster.predict	0.184	0.004	0.189
map.datasets	0.424	0.004	0.429
mod1	0.000	0.000	0.002
mod2	0.000	0.000	0.002
modelOvcAngiogenic	0.004	0.000	0.002
nkis	0.000	0.000	0.002
npi	0.004	0.000	0.006
oncotypedx	0.080	0.000	0.079
ovcAngiogenic	0.080	0.000	0.078
ovcCrijns	0.188	0.008	0.194
ovcTCGA	0.296	0.000	0.298
ovcYoshihara	0.064	0.004	0.067
pam50	0.02	0.00	0.02
pik3cags	0.072	0.000	0.073
power.cor	0.000	0.000	0.001
ps.cluster	0.680	0.004	0.671
read.m.file	0.036	0.000	0.036
rename.duplicate	0.004	0.000	0.003
rescale	0.028	0.004	0.033
rorS	0.184	0.000	0.186
scmgene.robust	0.004	0.000	0.005
scmod1.robust	0.008	0.000	0.006
scmod2.robust	0.008	0.000	0.006
setcolclass.df	0.004	0.000	0.003
sig.endoPredict	0.004	0.000	0.005
sig.gene70	0.004	0.000	0.006
sig.gene76	0.008	0.000	0.006
sig.genius	0.016	0.008	0.024
sig.ggi	0.004	0.000	0.007
sig.oncotypedx	0.004	0.000	0.004
sig.pik3cags	0.004	0.000	0.004
sig.score	0.084	0.000	0.082
sig.tamr13	0.000	0.004	0.006
sigOvcAngiogenic	0.004	0.004	0.007
sigOvcCrijns	0.012	0.000	0.013
sigOvcSpentzos	0.008	0.000	0.007
sigOvcTCGA	0.008	0.000	0.008
sigOvcYoshihara	0.008	0.000	0.007
spearmanCI	0.004	0.000	0.001
ssp2003	0.016	0.004	0.022
ssp2006	0.024	0.000	0.025
st.gallen	0.008	0.000	0.007
stab.fs	0.216	0.000	0.215
stab.fs.ranking	1.232	0.000	1.236
strescR	0.004	0.000	0.001
subtype.cluster	0.780	0.004	0.788
subtype.cluster.predict	0.136	0.008	0.144
tamr13	0.176	0.000	0.177
tbrm	0.000	0.000	0.001
vdxs	0.000	0.000	0.002
weighted.meanvar	0.004	0.000	0.001
write.m.file	0.000	0.000	0.002