BioC 3.2: CHECK report for genefu on oaxaca

Package: genefu

Version: 2.2.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.2.0.tar.gz

StartedAt: 2016-04-23 00:24:06 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:27:01 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 175.0 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 1

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.2.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genefu.Rcheck’
* using R version 3.2.4 (2016-03-10)
* using platform: x86_64-apple-darwin13.4.0 (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 ‘2.2.0’
* 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 ... [16s/19s] OK
* checking installed package size ... NOTE
  installed size is  6.1Mb
  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 loading without being on the library search path ... 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.
* checking S3 generic/method consistency ... WARNING
compare:
  function(obj, iC10, newdata, name.test, ...)
compare.proto.cor:
  function(gene.cor, proto.cor, nn, p.adjust.m)

See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
* 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 ... NOTE
S3 methods shown with full name in documentation object 'compare.proto.cor':
  ‘compare.proto.cor’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* 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 files in ‘vignettes’ ... OK
* checking examples ... [19s/20s] 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
* DONE

Status: 1 WARNING, 4 NOTEs
See
  ‘/Users/biocbuild/bbs-3.2-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	0.213	0.015	0.227
boxplotplus2	0.008	0.000	0.008
compare.proto.cor	0.877	0.018	0.895
compute.pairw.cor.meta	1.305	0.048	1.355
compute.proto.cor.meta	0.674	0.023	0.697
cordiff.dep	0.012	0.004	0.015
endoPredict	0.018	0.003	0.022
expos	0.003	0.002	0.004
fuzzy.ttest	0.002	0.000	0.003
gene70	0.167	0.009	0.176
gene76	0.042	0.003	0.045
geneid.map	0.080	0.005	0.086
genius	0.221	0.007	0.228
ggi	0.064	0.004	0.067
intrinsic.cluster	0.345	0.008	0.340
intrinsic.cluster.predict	0.218	0.006	0.225
map.datasets	0.604	0.013	0.619
mod1	0.002	0.001	0.004
mod2	0.002	0.000	0.002
modelOvcAngiogenic	0.001	0.001	0.003
molecular.subtyping	3.323	0.096	3.601
nkis	0.002	0.001	0.004
npi	0.006	0.003	0.009
oncotypedx	0.071	0.008	0.078
ovcAngiogenic	0.068	0.003	0.070
ovcCrijns	0.073	0.003	0.076
ovcTCGA	0.330	0.003	0.333
ovcYoshihara	0.077	0.004	0.082
pam50	0.023	0.002	0.027
pik3cags	0.063	0.003	0.067
power.cor	0.001	0.001	0.001
ps.cluster	0.678	0.014	0.664
read.m.file	0.040	0.001	0.040
rename.duplicate	0.003	0.001	0.003
rescale	0.026	0.003	0.029
rorS	0.214	0.008	0.222
scmgene.robust	0.006	0.002	0.008
scmod1.robust	0.008	0.001	0.009
scmod2.robust	0.007	0.002	0.009
setcolclass.df	0.002	0.000	0.002
sig.endoPredict	0.005	0.002	0.007
sig.gene70	0.007	0.002	0.008
sig.gene76	0.008	0.002	0.009
sig.genius	0.034	0.007	0.041
sig.ggi	0.008	0.002	0.010
sig.oncotypedx	0.005	0.001	0.005
sig.pik3cags	0.004	0.001	0.004
sig.score	0.088	0.005	0.093
sig.tamr13	0.006	0.002	0.007
sigOvcAngiogenic	0.009	0.001	0.010
sigOvcCrijns	0.008	0.001	0.009
sigOvcSpentzos	0.009	0.002	0.010
sigOvcTCGA	0.010	0.002	0.012
sigOvcYoshihara	0.009	0.002	0.010
spearmanCI	0.002	0.000	0.001
ssp2003	0.030	0.004	0.034
ssp2006	0.034	0.003	0.062
st.gallen	0.008	0.002	0.011
stab.fs	0.177	0.003	0.181
stab.fs.ranking	1.229	0.025	1.258
strescR	0.001	0.000	0.002
subtype.cluster	0.500	0.031	0.587
subtype.cluster.predict	0.139	0.009	0.150
tamr13	0.048	0.002	0.051
tbrm	0.001	0.000	0.002
vdxs	0.002	0.001	0.003
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.003	0.001	0.003