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: 2015-10-27 03:53:54 -0400 (Tue, 27 Oct 2015)

EndedAt: 2015-10-27 03:56:18 -0400 (Tue, 27 Oct 2015)

EllapsedTime: 143.6 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 3.2.2 (2015-08-14)
* 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 ... [13s/14s] 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 ... [17s/17s] 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	0.375	0.014	0.389
boxplotplus2	0.017	0.001	0.018
compare.proto.cor	0.697	0.011	0.709
compute.pairw.cor.meta	1.390	0.020	1.413
compute.proto.cor.meta	0.671	0.012	0.684
cordiff.dep	0.013	0.003	0.016
endoPredict	0.025	0.001	0.026
expos	0.002	0.000	0.003
fuzzy.ttest	0.003	0.000	0.003
gene70	0.170	0.007	0.176
gene76	0.058	0.001	0.059
geneid.map	0.081	0.003	0.084
genius	0.372	0.007	0.380
ggi	0.072	0.004	0.076
intrinsic.cluster	0.346	0.004	0.343
intrinsic.cluster.predict	0.234	0.005	0.240
map.datasets	0.456	0.009	0.465
mod1	0.002	0.000	0.002
mod2	0.002	0.001	0.003
modelOvcAngiogenic	0.003	0.001	0.003
molecular.subtyping	3.146	0.093	3.365
nkis	0.002	0.001	0.002
npi	0.007	0.002	0.008
oncotypedx	0.072	0.002	0.074
ovcAngiogenic	0.241	0.007	0.248
ovcCrijns	0.055	0.001	0.056
ovcTCGA	0.342	0.005	0.347
ovcYoshihara	0.066	0.002	0.068
pam50	0.023	0.002	0.025
pik3cags	0.065	0.002	0.068
power.cor	0.001	0.000	0.001
ps.cluster	0.646	0.014	0.635
read.m.file	0.045	0.001	0.046
rename.duplicate	0.002	0.000	0.003
rescale	0.022	0.001	0.024
rorS	0.214	0.004	0.218
scmgene.robust	0.006	0.001	0.007
scmod1.robust	0.006	0.001	0.007
scmod2.robust	0.006	0.000	0.006
setcolclass.df	0.003	0.000	0.002
sig.endoPredict	0.005	0.000	0.005
sig.gene70	0.007	0.001	0.007
sig.gene76	0.007	0.001	0.008
sig.genius	0.036	0.006	0.042
sig.ggi	0.008	0.001	0.008
sig.oncotypedx	0.005	0.001	0.006
sig.pik3cags	0.003	0.001	0.005
sig.score	0.079	0.003	0.082
sig.tamr13	0.006	0.002	0.008
sigOvcAngiogenic	0.007	0.001	0.008
sigOvcCrijns	0.007	0.001	0.008
sigOvcSpentzos	0.008	0.001	0.009
sigOvcTCGA	0.009	0.001	0.010
sigOvcYoshihara	0.008	0.001	0.009
spearmanCI	0.001	0.000	0.001
ssp2003	0.028	0.002	0.030
ssp2006	0.028	0.002	0.029
st.gallen	0.011	0.002	0.013
stab.fs	0.191	0.004	0.195
stab.fs.ranking	1.193	0.019	1.214
strescR	0.001	0.001	0.003
subtype.cluster	0.498	0.028	0.529
subtype.cluster.predict	0.153	0.005	0.158
tamr13	0.057	0.002	0.058
tbrm	0.001	0.000	0.001
vdxs	0.002	0.001	0.002
weighted.meanvar	0.000	0.000	0.001
write.m.file	0.002	0.001	0.002