BioC 3.2: CHECK report for genefu on oaxaca

Package: genefu

Version: 2.0.3

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_2.0.3.tar.gz

StartedAt: 2015-08-24 00:07:23 -0700 (Mon, 24 Aug 2015)

EndedAt: 2015-08-24 00:09:42 -0700 (Mon, 24 Aug 2015)

EllapsedTime: 139.2 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_2.0.3.tar.gz
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* 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 ‘2.0.3’
* 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	0.354	0.013	0.368
boxplotplus2	0.010	0.000	0.016
compare.proto.cor	0.666	0.016	0.682
compute.pairw.cor.meta	1.310	0.031	1.348
compute.proto.cor.meta	0.636	0.016	0.653
cordiff.dep	0.013	0.003	0.016
endoPredict	0.027	0.001	0.028
expos	0.002	0.000	0.003
fuzzy.ttest	0.002	0.001	0.003
gene70	0.177	0.008	0.184
gene76	0.053	0.001	0.054
geneid.map	0.072	0.003	0.075
genius	0.258	0.004	0.262
ggi	0.217	0.003	0.220
intrinsic.cluster	0.340	0.004	0.338
intrinsic.cluster.predict	0.227	0.003	0.230
map.datasets	0.475	0.009	0.484
mod1	0.001	0.001	0.002
mod2	0.002	0.000	0.003
modelOvcAngiogenic	0.002	0.001	0.003
molecular.subtyping	3.235	0.106	3.497
nkis	0.002	0.000	0.002
npi	0.007	0.002	0.009
oncotypedx	0.072	0.002	0.074
ovcAngiogenic	0.093	0.003	0.096
ovcCrijns	0.074	0.001	0.075
ovcTCGA	0.490	0.004	0.495
ovcYoshihara	0.062	0.001	0.063
pam50	0.022	0.001	0.024
pik3cags	0.066	0.005	0.071
power.cor	0.001	0.000	0.001
ps.cluster	0.662	0.013	0.646
read.m.file	0.043	0.001	0.043
rename.duplicate	0.003	0.000	0.003
rescale	0.025	0.001	0.026
rorS	0.200	0.006	0.207
scmgene.robust	0.006	0.001	0.006
scmod1.robust	0.007	0.001	0.007
scmod2.robust	0.007	0.000	0.007
setcolclass.df	0.003	0.000	0.002
sig.endoPredict	0.005	0.001	0.005
sig.gene70	0.006	0.000	0.007
sig.gene76	0.008	0.000	0.009
sig.genius	0.030	0.005	0.036
sig.ggi	0.007	0.001	0.008
sig.oncotypedx	0.004	0.001	0.005
sig.pik3cags	0.004	0.000	0.005
sig.score	0.086	0.003	0.089
sig.tamr13	0.006	0.003	0.009
sigOvcAngiogenic	0.007	0.000	0.008
sigOvcCrijns	0.007	0.000	0.009
sigOvcSpentzos	0.007	0.000	0.009
sigOvcTCGA	0.009	0.001	0.010
sigOvcYoshihara	0.006	0.001	0.006
spearmanCI	0.001	0.000	0.001
ssp2003	0.024	0.002	0.026
ssp2006	0.026	0.001	0.028
st.gallen	0.009	0.001	0.035
stab.fs	0.202	0.003	0.205
stab.fs.ranking	1.227	0.022	1.250
strescR	0.001	0.000	0.002
subtype.cluster	0.473	0.025	0.524
subtype.cluster.predict	0.131	0.008	0.141
tamr13	0.044	0.001	0.046
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	0.001	0.002