BioC 3.2: CHECK report for genefu on zin1

Package: genefu

Version: 2.2.0

Command: /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genefu_2.2.0.tar.gz

StartedAt: 2016-04-23 00:56:20 -0700 (Sat, 23 Apr 2016)

EndedAt: 2016-04-23 00:58:35 -0700 (Sat, 23 Apr 2016)

EllapsedTime: 135.5 seconds

RetCode: 0

Status:  WARNINGS

CheckDir: genefu.Rcheck

Warnings: 1

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### Running command:
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###   /home/biocbuild/bbs-3.2-bioc/R/bin/R CMD check --no-vignettes --timings genefu_2.2.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.2-bioc/meat/genefu.Rcheck’
* using R version 3.2.4 Revised (2016-03-16 r70336)
* using platform: x86_64-pc-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 ‘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 ... [12s/12s] OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  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 ... [16s/16s] 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
  ‘/home/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	0.473	0.004	0.477
boxplotplus2	0.008	0.000	0.009
compare.proto.cor	0.844	0.004	0.848
compute.pairw.cor.meta	1.235	0.004	1.259
compute.proto.cor.meta	0.648	0.008	0.660
cordiff.dep	0.014	0.000	0.014
endoPredict	0.020	0.000	0.019
expos	0.002	0.000	0.002
fuzzy.ttest	0.002	0.000	0.002
gene70	0.147	0.003	0.157
gene76	0.042	0.000	0.043
geneid.map	0.064	0.004	0.070
genius	0.200	0.000	0.212
ggi	0.063	0.003	0.068
intrinsic.cluster	0.282	0.000	0.265
intrinsic.cluster.predict	0.175	0.004	0.182
map.datasets	0.571	0.000	0.584
mod1	0.002	0.000	0.002
mod2	0.002	0.000	0.002
modelOvcAngiogenic	0.002	0.000	0.002
molecular.subtyping	3.062	0.009	3.283
nkis	0.002	0.000	0.002
npi	0.006	0.000	0.006
oncotypedx	0.073	0.000	0.077
ovcAngiogenic	0.062	0.000	0.067
ovcCrijns	0.070	0.000	0.069
ovcTCGA	0.251	0.000	0.257
ovcYoshihara	0.061	0.000	0.062
pam50	0.019	0.000	0.019
pik3cags	0.062	0.004	0.067
power.cor	0.000	0.000	0.001
ps.cluster	0.529	0.000	0.509
read.m.file	0.028	0.000	0.028
rename.duplicate	0.002	0.000	0.003
rescale	0.029	0.000	0.029
rorS	0.158	0.004	0.162
scmgene.robust	0.001	0.004	0.004
scmod1.robust	0.005	0.000	0.005
scmod2.robust	0.005	0.000	0.006
setcolclass.df	0.002	0.000	0.001
sig.endoPredict	0.004	0.000	0.004
sig.gene70	0.004	0.000	0.005
sig.gene76	0.005	0.000	0.005
sig.genius	0.015	0.004	0.019
sig.ggi	0.001	0.004	0.005
sig.oncotypedx	0.003	0.000	0.004
sig.pik3cags	0.003	0.000	0.003
sig.score	0.066	0.000	0.066
sig.tamr13	0.005	0.000	0.004
sigOvcAngiogenic	0.001	0.004	0.006
sigOvcCrijns	0.006	0.000	0.005
sigOvcSpentzos	0.005	0.000	0.005
sigOvcTCGA	0.006	0.000	0.006
sigOvcYoshihara	0.005	0.000	0.006
spearmanCI	0.000	0.004	0.001
ssp2003	0.017	0.000	0.019
ssp2006	0.025	0.008	0.033
st.gallen	0.007	0.000	0.008
stab.fs	0.137	0.000	0.139
stab.fs.ranking	0.939	0.004	0.950
strescR	0.001	0.000	0.001
subtype.cluster	0.431	0.008	0.441
subtype.cluster.predict	0.136	0.008	0.150
tamr13	0.037	0.000	0.039
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	0.001