BioC 2.14: CHECK report for genefu on morelia

Package: genefu

Version: 1.14.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --no-vignettes --timings --no-multiarch genefu_1.14.0.tar.gz

StartedAt: 2014-10-07 22:58:47 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 23:01:19 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 152.9 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 --no-multiarch genefu_1.14.0.tar.gz
###
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* using log directory ‘/Users/biocbuild/bbs-2.14-bioc/meat/genefu.Rcheck’
* using R version 3.1.1 (2014-07-10)
* using platform: x86_64-apple-darwin13.1.0 (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 ‘1.14.0’
* 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 ... [14s/16s] 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.
See the information on DESCRIPTION files in the chapter ‘Creating R
packages’ of the ‘Writing R Extensions’ manual.
* checking S3 generic/method consistency ... OK
* 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 ... 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 ... [15s/15s] 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

NOTE: There were 3 notes.
See
  ‘/Users/biocbuild/bbs-2.14-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	0.453	0.012	0.466
boxplotplus2	0.011	0.001	0.012
compare.proto.cor	0.785	0.018	0.807
compute.pairw.cor.meta	1.355	0.029	1.390
compute.proto.cor.meta	0.488	0.012	0.501
cordiff.dep	0.013	0.003	0.015
endoPredict	0.028	0.003	0.031
expos	0.001	0.000	0.002
fuzzy.ttest	0.002	0.001	0.002
gene70	0.170	0.004	0.174
gene76	0.046	0.001	0.048
geneid.map	0.203	0.004	0.209
genius	0.240	0.008	0.249
ggi	0.191	0.004	0.195
intrinsic.cluster	0.342	0.005	0.321
intrinsic.cluster.predict	0.214	0.004	0.218
map.datasets	0.447	0.008	0.457
mod1	0.002	0.000	0.002
mod2	0.002	0.000	0.003
modelOvcAngiogenic	0.003	0.000	0.003
nkis	0.002	0.000	0.001
npi	0.007	0.002	0.009
oncotypedx	0.088	0.006	0.094
ovcAngiogenic	0.081	0.001	0.082
ovcCrijns	0.090	0.001	0.091
ovcTCGA	0.488	0.004	0.494
ovcYoshihara	0.061	0.002	0.063
pam50	0.019	0.001	0.020
pik3cags	0.198	0.001	0.198
power.cor	0.001	0.001	0.001
ps.cluster	0.548	0.008	0.530
read.m.file	0.049	0.002	0.051
rename.duplicate	0.003	0.001	0.002
rescale	0.041	0.002	0.043
rorS	0.183	0.002	0.185
scmgene.robust	0.007	0.001	0.007
scmod1.robust	0.007	0.001	0.007
scmod2.robust	0.017	0.001	0.017
setcolclass.df	0.004	0.000	0.004
sig.endoPredict	0.005	0.001	0.005
sig.gene70	0.006	0.000	0.007
sig.gene76	0.007	0.001	0.008
sig.genius	0.037	0.006	0.043
sig.ggi	0.007	0.000	0.008
sig.oncotypedx	0.004	0.001	0.004
sig.pik3cags	0.003	0.000	0.003
sig.score	0.084	0.000	0.085
sig.tamr13	0.006	0.001	0.008
sigOvcAngiogenic	0.009	0.000	0.010
sigOvcCrijns	0.008	0.000	0.009
sigOvcSpentzos	0.007	0.000	0.008
sigOvcTCGA	0.009	0.001	0.009
sigOvcYoshihara	0.008	0.001	0.008
spearmanCI	0.001	0.000	0.001
ssp2003	0.026	0.002	0.028
ssp2006	0.027	0.001	0.029
st.gallen	0.008	0.002	0.009
stab.fs	0.220	0.003	0.226
stab.fs.ranking	1.337	0.018	1.365
strescR	0.001	0.000	0.001
subtype.cluster	0.822	0.016	0.844
subtype.cluster.predict	0.151	0.003	0.154
tamr13	0.055	0.000	0.056
tbrm	0.000	0.000	0.001
vdxs	0.001	0.000	0.001
weighted.meanvar	0.000	0.000	0.001
write.m.file	0.002	0.000	0.003