Package: genefu

Version: 2.15.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefu_2.15.0.tar.gz

StartedAt: 2019-04-09 01:03:31 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:06:15 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 164.0 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 --install=check:genefu.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings genefu_2.15.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2018-11-27 r75683)
* using platform: x86_64-apple-darwin15.6.0 (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 ‘2.15.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  'survcomp', 'mclust', 'limma', 'biomaRt', 'iC10', 'AIMS'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
* 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 ... OK
* checking installed package size ... NOTE
  installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
* 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.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
claudinLow: no visible global function definition for ‘standardize’
Undefined global functions or variables:
  standardize
* 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 files in ‘vignettes’ ... OK
* checking examples ... 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-3.9-bioc/meat/genefu.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genefu
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.6/Resources/library’
* installing *source* package ‘genefu’ ...
** R
** data
*** moving datasets to lazyload DB
** inst
** byte-compile and prepare 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	0.209	0.019	0.229
boxplotplus2	0.011	0.000	0.012
claudinLow	1.336	0.021	1.362
claudinLowData	0.032	0.004	0.036
compare.proto.cor	0.889	0.017	0.909
compute.pairw.cor.meta	1.492	0.063	1.562
compute.proto.cor.meta	0.850	0.037	0.891
cordiff.dep	0.013	0.002	0.015
endoPredict	0.022	0.003	0.025
expos	0.002	0.001	0.003
fuzzy.ttest	0.001	0.000	0.002
gene70	0.142	0.015	0.157
gene76	0.037	0.003	0.040
geneid.map	0.074	0.006	0.081
genius	0.175	0.025	0.202
ggi	0.071	0.008	0.080
ihc4	0.009	0.004	0.014
intrinsic.cluster	0.276	0.012	0.270
intrinsic.cluster.predict	0.186	0.011	0.198
map.datasets	0.773	0.016	0.796
mod1	0.002	0.001	0.003
mod2	0.002	0.001	0.004
modelOvcAngiogenic	0.002	0.002	0.003
molecular.subtyping	2.938	0.121	3.082
nkis	0.002	0.002	0.004
npi	0.007	0.005	0.012
oncotypedx	0.080	0.005	0.086
ovcAngiogenic	0.074	0.009	0.083
ovcCrijns	0.099	0.011	0.111
ovcTCGA	0.311	0.006	0.318
ovcYoshihara	0.074	0.009	0.085
pam50	0.032	0.005	0.037
pik3cags	0.095	0.007	0.103
power.cor	0.001	0.000	0.001
ps.cluster	0.458	0.012	0.450
read.m.file	0.032	0.002	0.034
rename.duplicate	0.002	0.000	0.003
rescale	0.047	0.004	0.052
rorS	0.164	0.007	0.171
scmgene.robust	0.008	0.002	0.010
scmod1.robust	0.008	0.003	0.011
scmod2.robust	0.010	0.003	0.012
setcolclass.df	0.002	0.000	0.003
sig.endoPredict	0.006	0.002	0.008
sig.gene70	0.007	0.002	0.009
sig.gene76	0.005	0.002	0.008
sig.genius	0.037	0.012	0.049
sig.ggi	0.007	0.002	0.008
sig.oncotypedx	0.005	0.002	0.008
sig.pik3cags	0.004	0.003	0.007
sig.score	0.069	0.004	0.073
sig.tamr13	0.008	0.005	0.012
sigOvcAngiogenic	0.008	0.002	0.011
sigOvcCrijns	0.008	0.002	0.012
sigOvcSpentzos	0.008	0.002	0.010
sigOvcTCGA	0.010	0.003	0.012
sigOvcYoshihara	0.007	0.003	0.010
spearmanCI	0.000	0.000	0.001
ssp2003	0.039	0.005	0.045
ssp2006	0.045	0.005	0.050
st.gallen	0.009	0.003	0.013
stab.fs	0.132	0.004	0.137
stab.fs.ranking	0.969	0.046	1.017
strescR	0.001	0.000	0.002
subtype.cluster	0.495	0.044	0.550
subtype.cluster.predict	0.171	0.020	0.192
tamr13	0.048	0.005	0.052
tbrm	0.001	0.000	0.000
vdxs	0.002	0.002	0.004
weighted.meanvar	0.001	0.000	0.000
write.m.file	0.003	0.002	0.004