BioC 3.1: CHECK report for genefu on petty

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: 2015-10-08 23:10:05 -0700 (Thu, 08 Oct 2015)

EndedAt: 2015-10-08 23:13:14 -0700 (Thu, 08 Oct 2015)

EllapsedTime: 189.4 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 Patched (2015-08-14 r69078)
* 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 ‘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 ... [19s/20s] 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 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 ... [22s/22s] 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	0.587	0.023	0.610
boxplotplus2	0.028	0.001	0.030
compare.proto.cor	1.093	0.027	1.121
compute.pairw.cor.meta	2.105	0.054	2.162
compute.proto.cor.meta	0.821	0.023	0.845
cordiff.dep	0.022	0.004	0.026
endoPredict	0.038	0.002	0.040
expos	0.002	0.000	0.002
fuzzy.ttest	0.003	0.000	0.003
gene70	0.461	0.011	0.472
gene76	0.055	0.002	0.056
geneid.map	0.147	0.007	0.156
genius	0.396	0.011	0.406
ggi	0.109	0.004	0.114
intrinsic.cluster	0.532	0.023	0.510
intrinsic.cluster.predict	0.573	0.026	0.599
map.datasets	0.762	0.022	0.784
mod1	0.002	0.000	0.003
mod2	0.002	0.001	0.002
modelOvcAngiogenic	0.004	0.001	0.004
nkis	0.003	0.000	0.004
npi	0.010	0.003	0.014
oncotypedx	0.114	0.008	0.122
ovcAngiogenic	0.129	0.007	0.136
ovcCrijns	0.123	0.004	0.126
ovcTCGA	0.707	0.008	0.716
ovcYoshihara	0.111	0.003	0.114
pam50	0.031	0.002	0.033
pik3cags	0.111	0.003	0.114
power.cor	0.001	0.000	0.002
ps.cluster	0.962	0.030	0.956
read.m.file	0.059	0.004	0.063
rename.duplicate	0.003	0.000	0.003
rescale	0.043	0.003	0.076
rorS	0.302	0.010	0.312
scmgene.robust	0.007	0.001	0.008
scmod1.robust	0.009	0.001	0.009
scmod2.robust	0.008	0.001	0.009
setcolclass.df	0.005	0.001	0.005
sig.endoPredict	0.008	0.001	0.008
sig.gene70	0.022	0.002	0.024
sig.gene76	0.010	0.001	0.011
sig.genius	0.059	0.009	0.068
sig.ggi	0.010	0.000	0.011
sig.oncotypedx	0.007	0.001	0.007
sig.pik3cags	0.005	0.001	0.007
sig.score	0.133	0.003	0.137
sig.tamr13	0.009	0.002	0.011
sigOvcAngiogenic	0.011	0.001	0.013
sigOvcCrijns	0.009	0.001	0.011
sigOvcSpentzos	0.010	0.001	0.011
sigOvcTCGA	0.027	0.002	0.030
sigOvcYoshihara	0.012	0.001	0.014
spearmanCI	0.001	0.000	0.001
ssp2003	0.039	0.002	0.042
ssp2006	0.051	0.002	0.053
st.gallen	0.014	0.003	0.016
stab.fs	0.289	0.003	0.293
stab.fs.ranking	1.755	0.067	1.823
strescR	0.003	0.001	0.002
subtype.cluster	1.058	0.045	1.111
subtype.cluster.predict	0.469	0.011	0.480
tamr13	0.081	0.002	0.083
tbrm	0.001	0.000	0.002
vdxs	0.002	0.000	0.002
weighted.meanvar	0.001	0.001	0.002
write.m.file	0.003	0.000	0.004