BioC 3.1: CHECK report for genefu on morelia

Package: genefu

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings genefu_1.18.0.tar.gz

StartedAt: 2015-10-09 02:09:50 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:12:00 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 130.2 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

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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_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.1-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 ‘1.18.0’
* 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/13s] 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 ... NOTE
Malformed Title field: should not end in a period.
* 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: ‘multilevel’, ‘dplR’
* 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 ... [13s/14s] 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: 5 NOTEs
See
  ‘/Users/biocbuild/bbs-3.1-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
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
Creating a generic function for ‘nchar’ from package ‘base’ in package ‘S4Vectors’
* DONE (genefu)

name	user	system	elapsed
bimod	0.349	0.034	0.384
boxplotplus2	0.016	0.000	0.016
compare.proto.cor	0.667	0.047	0.716
compute.pairw.cor.meta	1.272	0.065	1.341
compute.proto.cor.meta	0.480	0.027	0.507
cordiff.dep	0.013	0.003	0.016
endoPredict	0.021	0.000	0.022
expos	0.002	0.001	0.002
fuzzy.ttest	0.003	0.000	0.003
gene70	0.125	0.005	0.130
gene76	0.041	0.010	0.051
geneid.map	0.071	0.018	0.090
genius	0.215	0.017	0.306
ggi	0.176	0.021	0.197
intrinsic.cluster	0.253	0.051	0.418
intrinsic.cluster.predict	0.167	0.028	0.195
map.datasets	0.363	0.005	0.369
mod1	0.001	0.000	0.001
mod2	0.002	0.000	0.002
modelOvcAngiogenic	0.002	0.001	0.002
nkis	0.001	0.000	0.001
npi	0.004	0.001	0.005
oncotypedx	0.060	0.004	0.063
ovcAngiogenic	0.063	0.002	0.065
ovcCrijns	0.062	0.001	0.063
ovcTCGA	0.247	0.015	0.263
ovcYoshihara	0.057	0.001	0.058
pam50	0.013	0.000	0.014
pik3cags	0.057	0.001	0.058
power.cor	0.000	0.000	0.001
ps.cluster	0.686	0.104	0.775
read.m.file	0.037	0.009	0.046
rename.duplicate	0.003	0.000	0.003
rescale	0.019	0.001	0.021
rorS	0.184	0.013	0.222
scmgene.robust	0.005	0.001	0.006
scmod1.robust	0.005	0.002	0.007
scmod2.robust	0.006	0.002	0.007
setcolclass.df	0.004	0.001	0.005
sig.endoPredict	0.005	0.003	0.008
sig.gene70	0.005	0.003	0.009
sig.gene76	0.008	0.000	0.008
sig.genius	0.035	0.014	0.050
sig.ggi	0.005	0.001	0.005
sig.oncotypedx	0.004	0.000	0.005
sig.pik3cags	0.003	0.001	0.003
sig.score	0.067	0.001	0.068
sig.tamr13	0.005	0.002	0.007
sigOvcAngiogenic	0.006	0.000	0.006
sigOvcCrijns	0.008	0.000	0.008
sigOvcSpentzos	0.008	0.001	0.008
sigOvcTCGA	0.009	0.001	0.010
sigOvcYoshihara	0.008	0.001	0.009
spearmanCI	0.001	0.000	0.001
ssp2003	0.021	0.001	0.023
ssp2006	0.027	0.002	0.027
st.gallen	0.008	0.001	0.009
stab.fs	0.179	0.012	0.190
stab.fs.ranking	0.850	0.046	0.896
strescR	0.001	0.000	0.001
subtype.cluster	0.368	0.021	0.450
subtype.cluster.predict	0.242	0.009	0.259
tamr13	0.042	0.002	0.045
tbrm	0	0	0
vdxs	0.001	0.000	0.002
weighted.meanvar	0.000	0.000	0.001
write.m.file	0.001	0.000	0.001