BioC 3.0: CHECK report for genefu on oaxaca

Package: genefu

Version: 1.16.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.16.0.tar.gz

StartedAt: 2015-04-09 23:46:23 -0700 (Thu, 09 Apr 2015)

EndedAt: 2015-04-09 23:49:22 -0700 (Thu, 09 Apr 2015)

EllapsedTime: 179.3 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.16.0.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.0-bioc/meat/genefu.Rcheck’
* using R version 3.1.3 (2015-03-09)
* 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 ‘1.16.0’
* 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 ... [17s/17s] OK
* checking installed package size ... NOTE
  installed size is  5.9Mb
  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 ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
endoPredict: no visible binding for global variable ‘sig.endoPredict’
gene70: no visible binding for global variable ‘sig.gene70’
gene76: no visible binding for global variable ‘sig.gene76’
genius: no visible binding for global variable ‘scmod1.robust’
genius: no visible binding for global variable ‘sig.genius’
ggi: no visible binding for global variable ‘sig.ggi’
oncotypedx: no visible binding for global variable ‘sig.oncotypedx’
ovcAngiogenic: no visible binding for global variable
  ‘sigOvcAngiogenic’
ovcAngiogenic: no visible binding for global variable
  ‘modelOvcAngiogenic’
ovcCrijns: no visible binding for global variable ‘sigOvcCrijns’
ovcTCGA: no visible binding for global variable ‘sigOvcTCGA’
ovcYoshihara: no visible binding for global variable ‘sigOvcYoshihara’
pik3cags: no visible binding for global variable ‘sig.pik3cags’
rorS: no visible binding for global variable ‘pam50’
subtype.cluster: no visible global function definition for ‘unmap’
subtype.cluster: no visible global function definition for
  ‘mclust.options’
subtype.cluster.predict: no visible global function definition for
  ‘unmap’
tamr13: no visible binding for global variable ‘sig.tamr13’
* checking Rd files ... OK
* checking Rd metadata ... OK
* checking Rd cross-references ... NOTE
Packages unavailable to check Rd xrefs: ‘dplR’, ‘multilevel’
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... OK
* 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/18s] 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

NOTE: There were 4 notes.
See
  ‘/Users/biocbuild/bbs-3.0-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	0.503	0.015	0.527
boxplotplus2	0.010	0.001	0.010
compare.proto.cor	0.742	0.019	0.775
compute.pairw.cor.meta	1.501	0.030	1.572
compute.proto.cor.meta	0.570	0.016	0.593
cordiff.dep	0.014	0.002	0.017
endoPredict	0.027	0.001	0.029
expos	0.002	0.000	0.002
fuzzy.ttest	0.002	0.001	0.003
gene70	0.324	0.007	0.346
gene76	0.048	0.001	0.052
geneid.map	0.106	0.003	0.118
genius	0.415	0.006	0.447
ggi	0.082	0.002	0.084
intrinsic.cluster	0.357	0.007	0.341
intrinsic.cluster.predict	0.359	0.003	0.367
map.datasets	0.488	0.010	0.510
mod1	0.002	0.000	0.003
mod2	0.002	0.001	0.003
modelOvcAngiogenic	0.002	0.000	0.003
nkis	0.002	0.000	0.002
npi	0.007	0.002	0.009
oncotypedx	0.091	0.004	0.096
ovcAngiogenic	0.106	0.002	0.111
ovcCrijns	0.233	0.002	0.238
ovcTCGA	0.375	0.003	0.384
ovcYoshihara	0.084	0.001	0.086
pam50	0.022	0.002	0.024
pik3cags	0.072	0.002	0.074
power.cor	0.001	0.000	0.001
ps.cluster	0.843	0.008	0.840
read.m.file	0.053	0.002	0.056
rename.duplicate	0.002	0.001	0.003
rescale	0.035	0.001	0.037
rorS	0.217	0.003	0.223
scmgene.robust	0.006	0.001	0.007
scmod1.robust	0.006	0.001	0.007
scmod2.robust	0.006	0.000	0.007
setcolclass.df	0.004	0.001	0.004
sig.endoPredict	0.005	0.000	0.006
sig.gene70	0.007	0.001	0.007
sig.gene76	0.008	0.001	0.008
sig.genius	0.040	0.006	0.047
sig.ggi	0.008	0.000	0.009
sig.oncotypedx	0.005	0.001	0.006
sig.pik3cags	0.004	0.001	0.005
sig.score	0.091	0.001	0.094
sig.tamr13	0.006	0.002	0.008
sigOvcAngiogenic	0.009	0.001	0.009
sigOvcCrijns	0.008	0.001	0.008
sigOvcSpentzos	0.007	0.001	0.009
sigOvcTCGA	0.009	0.001	0.010
sigOvcYoshihara	0.009	0.000	0.009
spearmanCI	0.001	0.000	0.001
ssp2003	0.027	0.001	0.029
ssp2006	0.032	0.002	0.033
st.gallen	0.009	0.002	0.011
stab.fs	0.222	0.007	0.234
stab.fs.ranking	1.397	0.019	1.439
strescR	0.002	0.000	0.002
subtype.cluster	0.578	0.019	0.622
subtype.cluster.predict	0.328	0.005	0.336
tamr13	0.056	0.002	0.058
tbrm	0.001	0.000	0.001
vdxs	0.003	0.000	0.002
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.003	0.001	0.002