Package: genefu

Version: 2.16.0

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_2.16.0.tar.gz

StartedAt: 2019-10-16 03:03:08 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 03:06:39 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 211.8 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_2.16.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck’
* using R version 3.6.1 (2019-07-05)
* 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 ‘2.16.0’
* 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’ ...
** using staged installation
** 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 from temporary location
** testing if installed package can be loaded from final location
** testing if installed package keeps a record of temporary installation path
* DONE (genefu)

name	user	system	elapsed
bimod	0.233	0.036	0.270
boxplotplus2	0.014	0.001	0.015
claudinLow	1.504	0.053	1.557
claudinLowData	0.027	0.008	0.035
compare.proto.cor	1.185	0.041	1.226
compute.pairw.cor.meta	1.750	0.108	1.860
compute.proto.cor.meta	1.041	0.047	1.088
cordiff.dep	0.014	0.003	0.018
endoPredict	0.024	0.009	0.034
expos	0.002	0.004	0.006
fuzzy.ttest	0.001	0.001	0.003
gene70	0.202	0.032	0.234
gene76	0.061	0.013	0.074
geneid.map	0.075	0.012	0.086
genius	0.308	0.058	0.367
ggi	0.079	0.012	0.092
ihc4	0.015	0.010	0.026
intrinsic.cluster	0.385	0.033	0.391
intrinsic.cluster.predict	0.268	0.036	0.303
map.datasets	0.945	0.031	0.976
mod1	0.003	0.004	0.007
mod2	0.003	0.004	0.007
modelOvcAngiogenic	0.004	0.004	0.008
molecular.subtyping	3.835	0.288	4.137
nkis	0.003	0.003	0.006
npi	0.011	0.008	0.018
oncotypedx	0.082	0.014	0.096
ovcAngiogenic	0.112	0.023	0.135
ovcCrijns	0.065	0.007	0.072
ovcTCGA	0.321	0.016	0.336
ovcYoshihara	0.114	0.029	0.143
pam50	0.035	0.010	0.045
pik3cags	0.087	0.013	0.099
power.cor	0.001	0.001	0.001
ps.cluster	0.477	0.035	0.490
read.m.file	0.039	0.003	0.043
rename.duplicate	0.002	0.001	0.003
rescale	0.041	0.007	0.048
rorS	0.208	0.018	0.227
scmgene.robust	0.009	0.004	0.012
scmod1.robust	0.011	0.004	0.014
scmod2.robust	0.007	0.004	0.011
setcolclass.df	0.004	0.001	0.004
sig.endoPredict	0.008	0.005	0.012
sig.gene70	0.008	0.004	0.012
sig.gene76	0.008	0.004	0.013
sig.genius	0.048	0.019	0.067
sig.ggi	0.009	0.004	0.013
sig.oncotypedx	0.007	0.005	0.012
sig.pik3cags	0.006	0.004	0.010
sig.score	0.069	0.010	0.079
sig.tamr13	0.008	0.005	0.013
sigOvcAngiogenic	0.007	0.003	0.010
sigOvcCrijns	0.007	0.003	0.010
sigOvcSpentzos	0.006	0.003	0.010
sigOvcTCGA	0.012	0.004	0.015
sigOvcYoshihara	0.011	0.004	0.015
spearmanCI	0.001	0.000	0.001
ssp2003	0.050	0.009	0.059
ssp2006	0.064	0.009	0.074
st.gallen	0.013	0.008	0.020
stab.fs	0.171	0.005	0.176
stab.fs.ranking	1.292	0.175	1.467
strescR	0.001	0.000	0.001
subtype.cluster	0.454	0.059	0.516
subtype.cluster.predict	0.167	0.035	0.203
tamr13	0.084	0.018	0.101
tbrm	0.000	0.001	0.001
vdxs	0.002	0.004	0.006
weighted.meanvar	0.000	0.001	0.001
write.m.file	0.002	0.003	0.006