Package: genefu

Version: 2.19.0

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_2.19.0.tar.gz

StartedAt: 2020-01-16 04:44:12 -0500 (Thu, 16 Jan 2020)

EndedAt: 2020-01-16 04:48:18 -0500 (Thu, 16 Jan 2020)

EllapsedTime: 245.8 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_2.19.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.11-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2019-12-14 r77572)
* 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 ‘2.19.0’
* 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
Package unavailable to check Rd xrefs: ‘multilevel’
* 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-3.11-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/4.0/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	0.205	0.034	0.240
boxplotplus2	0.013	0.002	0.015
claudinLow	2.079	0.089	2.170
claudinLowData	0.039	0.012	0.052
compare.proto.cor	1.167	0.043	1.210
compute.pairw.cor.meta	1.891	0.138	2.029
compute.proto.cor.meta	1.008	0.053	1.061
cordiff.dep	0.013	0.003	0.016
endoPredict	0.021	0.007	0.028
expos	0.003	0.004	0.007
fuzzy.ttest	0.002	0.001	0.003
gene70	0.171	0.025	0.196
gene76	0.052	0.015	0.067
geneid.map	0.113	0.025	0.139
genius	0.265	0.050	0.316
ggi	0.063	0.019	0.083
ihc4	0.009	0.006	0.015
intrinsic.cluster	0.327	0.037	0.342
intrinsic.cluster.predict	0.211	0.027	0.239
map.datasets	1.026	0.038	1.064
mod1	0.003	0.003	0.007
mod2	0.003	0.004	0.007
modelOvcAngiogenic	0.003	0.004	0.008
molecular.subtyping	3.662	0.288	3.959
nkis	0.002	0.003	0.005
npi	0.007	0.006	0.013
oncotypedx	0.094	0.034	0.126
ovcAngiogenic	0.060	0.006	0.065
ovcCrijns	0.061	0.012	0.073
ovcTCGA	0.225	0.014	0.239
ovcYoshihara	0.121	0.036	0.157
pam50	0.042	0.010	0.053
pik3cags	0.065	0.009	0.074
power.cor	0.001	0.000	0.001
ps.cluster	0.526	0.038	0.544
read.m.file	0.042	0.004	0.047
rename.duplicate	0.003	0.001	0.004
rescale	0.061	0.011	0.073
rorS	0.204	0.018	0.222
scmgene.robust	0.009	0.005	0.015
scmod1.robust	0.009	0.003	0.012
scmod2.robust	0.011	0.004	0.015
setcolclass.df	0.003	0.000	0.003
sig.endoPredict	0.006	0.004	0.010
sig.gene70	0.009	0.004	0.012
sig.gene76	0.010	0.005	0.016
sig.genius	0.051	0.021	0.072
sig.ggi	0.009	0.004	0.014
sig.oncotypedx	0.005	0.003	0.009
sig.pik3cags	0.005	0.005	0.011
sig.score	0.139	0.030	0.169
sig.tamr13	0.009	0.008	0.018
sigOvcAngiogenic	0.014	0.004	0.018
sigOvcCrijns	0.009	0.004	0.014
sigOvcSpentzos	0.006	0.004	0.010
sigOvcTCGA	0.007	0.003	0.011
sigOvcYoshihara	0.007	0.003	0.010
spearmanCI	0.001	0.000	0.001
ssp2003	0.037	0.008	0.045
ssp2006	0.043	0.007	0.050
st.gallen	0.012	0.009	0.023
stab.fs	0.171	0.003	0.173
stab.fs.ranking	1.370	0.160	1.531
strescR	0.001	0.000	0.001
subtype.cluster	0.529	0.064	0.596
subtype.cluster.predict	0.198	0.047	0.245
tamr13	0.058	0.014	0.072
tbrm	0.001	0.000	0.002
vdxs	0.003	0.005	0.008
weighted.meanvar	0.001	0.001	0.001
write.m.file	0.003	0.005	0.009