BioC 3.2: CHECK report for genefu on perceval

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: 2015-11-10 05:06:09 -0800 (Tue, 10 Nov 2015)

EndedAt: 2015-11-10 05:08:36 -0800 (Tue, 10 Nov 2015)

EllapsedTime: 146.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 1

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.2.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.2-bioc/meat/genefu.Rcheck’
* using R version 3.2.2 Patched (2015-10-08 r69496)
* using platform: x86_64-apple-darwin10.8.0 (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 ... [14s/15s] 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 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 ... [20s/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	0.465	0.020	0.485
boxplotplus2	0.011	0.000	0.012
compare.proto.cor	0.868	0.022	0.891
compute.pairw.cor.meta	1.635	0.050	1.685
compute.proto.cor.meta	0.645	0.021	0.665
cordiff.dep	0.016	0.003	0.020
endoPredict	0.209	0.003	0.212
expos	0.001	0.000	0.002
fuzzy.ttest	0.002	0.000	0.003
gene70	0.187	0.009	0.197
gene76	0.049	0.002	0.051
geneid.map	0.095	0.004	0.099
genius	0.275	0.011	0.285
ggi	0.091	0.003	0.093
intrinsic.cluster	0.364	0.017	0.351
intrinsic.cluster.predict	0.243	0.010	0.253
map.datasets	0.593	0.016	0.608
mod1	0.002	0.000	0.002
mod2	0.002	0.001	0.002
modelOvcAngiogenic	0.002	0.001	0.003
molecular.subtyping	3.657	0.166	3.984
nkis	0.002	0.001	0.002
npi	0.007	0.002	0.009
oncotypedx	0.089	0.004	0.094
ovcAngiogenic	0.086	0.005	0.090
ovcCrijns	0.096	0.003	0.098
ovcTCGA	0.326	0.002	0.327
ovcYoshihara	0.081	0.004	0.084
pam50	0.022	0.002	0.023
pik3cags	0.081	0.003	0.084
power.cor	0.001	0.000	0.002
ps.cluster	0.696	0.020	0.686
read.m.file	0.038	0.002	0.041
rename.duplicate	0.003	0.000	0.003
rescale	0.032	0.004	0.035
rorS	0.210	0.003	0.213
scmgene.robust	0.005	0.000	0.006
scmod1.robust	0.006	0.001	0.007
scmod2.robust	0.006	0.001	0.006
setcolclass.df	0.003	0.000	0.003
sig.endoPredict	0.005	0.001	0.006
sig.gene70	0.006	0.001	0.007
sig.gene76	0.007	0.001	0.009
sig.genius	0.055	0.008	0.063
sig.ggi	0.007	0.001	0.009
sig.oncotypedx	0.004	0.001	0.005
sig.pik3cags	0.004	0.000	0.004
sig.score	0.087	0.003	0.089
sig.tamr13	0.007	0.003	0.009
sigOvcAngiogenic	0.009	0.001	0.009
sigOvcCrijns	0.007	0.001	0.008
sigOvcSpentzos	0.007	0.001	0.008
sigOvcTCGA	0.030	0.011	0.041
sigOvcYoshihara	0.008	0.000	0.009
spearmanCI	0.002	0.000	0.001
ssp2003	0.027	0.003	0.031
ssp2006	0.032	0.001	0.033
st.gallen	0.011	0.003	0.014
stab.fs	0.211	0.011	0.223
stab.fs.ranking	1.294	0.046	1.340
strescR	0.001	0.000	0.002
subtype.cluster	0.525	0.038	0.677
subtype.cluster.predict	0.354	0.015	0.493
tamr13	0.043	0.002	0.045
tbrm	0.001	0.000	0.001
vdxs	0.002	0.000	0.002
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.002	0.000	0.003