Package: genefu

Version: 2.18.1

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_2.18.1.tar.gz

StartedAt: 2020-04-15 02:32:02 -0400 (Wed, 15 Apr 2020)

EndedAt: 2020-04-15 02:34:54 -0400 (Wed, 15 Apr 2020)

EllapsedTime: 171.5 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

##############################################################################
##############################################################################
###
### Running 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_2.18.1.tar.gz
###
##############################################################################
##############################################################################


* using log directory ‘/Users/biocbuild/bbs-3.10-bioc/meat/genefu.Rcheck’
* using R version 3.6.3 (2020-02-29)
* 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 ‘2.18.1’
* 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 ... NOTE
Found the following hidden files and directories:
  .travis.yml
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
* 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: 6 NOTEs
See
  ‘/Users/biocbuild/bbs-3.10-bioc/meat/genefu.Rcheck/00check.log’
for details.

##############################################################################
##############################################################################
###
### Running command:
###
###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL genefu
###
##############################################################################
##############################################################################


* 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	0.187	0.015	0.202
boxplotplus2	0.009	0.001	0.010
claudinLow	1.462	0.046	1.514
claudinLowData	0.027	0.006	0.032
compare.proto.cor	0.883	0.021	0.911
compute.pairw.cor.meta	1.211	0.037	1.251
compute.proto.cor.meta	0.797	0.020	0.819
cordiff.dep	0.011	0.002	0.012
endoPredict	0.020	0.005	0.026
expos	0.002	0.002	0.004
fuzzy.ttest	0.002	0.000	0.001
gene70	0.138	0.016	0.158
gene76	0.035	0.003	0.038
geneid.map	0.060	0.007	0.068
genius	0.194	0.013	0.209
ggi	0.062	0.006	0.069
ihc4	0.009	0.004	0.013
intrinsic.cluster	0.257	0.013	0.252
intrinsic.cluster.predict	0.153	0.008	0.162
map.datasets	0.731	0.019	0.753
mod1	0.001	0.001	0.003
mod2	0.001	0.002	0.003
modelOvcAngiogenic	0.002	0.002	0.004
molecular.subtyping	2.643	0.135	2.791
nkis	0.001	0.001	0.003
npi	0.007	0.004	0.012
oncotypedx	0.063	0.005	0.068
ovcAngiogenic	0.081	0.009	0.089
ovcCrijns	0.053	0.005	0.059
ovcTCGA	0.225	0.007	0.232
ovcYoshihara	0.066	0.009	0.074
pam50	0.021	0.004	0.025
pik3cags	0.073	0.007	0.080
power.cor	0.000	0.000	0.001
ps.cluster	0.406	0.015	0.405
read.m.file	0.028	0.002	0.030
rename.duplicate	0.003	0.001	0.004
rescale	0.052	0.005	0.063
rorS	0.155	0.007	0.163
scmgene.robust	0.005	0.002	0.006
scmod1.robust	0.008	0.002	0.010
scmod2.robust	0.008	0.002	0.010
setcolclass.df	0.002	0.000	0.003
sig.endoPredict	0.004	0.002	0.007
sig.gene70	0.004	0.002	0.006
sig.gene76	0.008	0.003	0.010
sig.genius	0.047	0.012	0.060
sig.ggi	0.005	0.002	0.008
sig.oncotypedx	0.005	0.002	0.007
sig.pik3cags	0.004	0.002	0.006
sig.score	0.071	0.005	0.078
sig.tamr13	0.008	0.005	0.013
sigOvcAngiogenic	0.008	0.002	0.011
sigOvcCrijns	0.005	0.002	0.007
sigOvcSpentzos	0.008	0.002	0.010
sigOvcTCGA	0.007	0.002	0.010
sigOvcYoshihara	0.007	0.002	0.009
spearmanCI	0.001	0.000	0.001
ssp2003	0.033	0.004	0.038
ssp2006	0.057	0.005	0.062
st.gallen	0.008	0.004	0.014
stab.fs	0.135	0.004	0.142
stab.fs.ranking	1.001	0.039	1.049
strescR	0.001	0.001	0.000
subtype.cluster	0.474	0.042	0.520
subtype.cluster.predict	0.119	0.012	0.131
tamr13	0.040	0.005	0.046
tbrm	0.001	0.000	0.001
vdxs	0.001	0.001	0.003
weighted.meanvar	0.001	0.000	0.001
write.m.file	0.002	0.002	0.005