BioC 2.14: CHECK report for genefu on petty

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 22:06:18 -0700 (Tue, 07 Oct 2014)

EndedAt: 2014-10-07 22:10:41 -0700 (Tue, 07 Oct 2014)

EllapsedTime: 262.5 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-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 ‘1.14.0’
* 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 ... [24s/26s] 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 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 ... [28s/29s] 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	0.800	0.029	0.887
boxplotplus2	0.027	0.001	0.032
compare.proto.cor	1.432	0.037	1.489
compute.pairw.cor.meta	2.571	0.055	2.675
compute.proto.cor.meta	0.921	0.023	0.954
cordiff.dep	0.024	0.005	0.028
endoPredict	0.046	0.004	0.051
expos	0.003	0.000	0.004
fuzzy.ttest	0.004	0.000	0.005
gene70	0.306	0.008	0.319
gene76	0.083	0.002	0.089
geneid.map	0.399	0.008	0.415
genius	0.424	0.009	0.440
ggi	0.142	0.003	0.146
intrinsic.cluster	0.856	0.031	0.855
intrinsic.cluster.predict	0.379	0.018	0.401
map.datasets	0.804	0.021	0.836
mod1	0.003	0.000	0.004
mod2	0.003	0.000	0.004
modelOvcAngiogenic	0.004	0.000	0.005
nkis	0.003	0.000	0.004
npi	0.012	0.003	0.015
oncotypedx	0.397	0.018	0.421
ovcAngiogenic	0.134	0.005	0.142
ovcCrijns	0.143	0.004	0.147
ovcTCGA	0.635	0.008	0.650
ovcYoshihara	0.133	0.008	0.142
pam50	0.035	0.003	0.039
pik3cags	0.132	0.003	0.136
power.cor	0.002	0.000	0.002
ps.cluster	1.414	0.028	1.408
read.m.file	0.073	0.004	0.080
rename.duplicate	0.004	0.001	0.004
rescale	0.060	0.003	0.065
rorS	0.372	0.007	0.381
scmgene.robust	0.009	0.001	0.009
scmod1.robust	0.010	0.000	0.011
scmod2.robust	0.010	0.001	0.013
setcolclass.df	0.007	0.000	0.007
sig.endoPredict	0.008	0.001	0.009
sig.gene70	0.010	0.001	0.011
sig.gene76	0.013	0.001	0.013
sig.genius	0.073	0.013	0.086
sig.ggi	0.014	0.001	0.014
sig.oncotypedx	0.008	0.001	0.008
sig.pik3cags	0.007	0.001	0.007
sig.score	0.160	0.007	0.167
sig.tamr13	0.011	0.004	0.014
sigOvcAngiogenic	0.013	0.001	0.014
sigOvcCrijns	0.012	0.001	0.013
sigOvcSpentzos	0.012	0.001	0.013
sigOvcTCGA	0.014	0.001	0.015
sigOvcYoshihara	0.017	0.001	0.019
spearmanCI	0.002	0.001	0.002
ssp2003	0.045	0.003	0.047
ssp2006	0.053	0.003	0.056
st.gallen	0.028	0.003	0.032
stab.fs	0.435	0.007	0.446
stab.fs.ranking	2.611	0.041	2.706
strescR	0.003	0.000	0.003
subtype.cluster	1.144	0.041	1.378
subtype.cluster.predict	0.491	0.010	0.522
tamr13	0.092	0.004	0.097
tbrm	0.001	0.000	0.001
vdxs	0.003	0.001	0.004
weighted.meanvar	0.001	0.001	0.002
write.m.file	0.004	0.001	0.005