Package: genefu

Version: 2.16.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genefu_2.16.0.tar.gz

StartedAt: 2019-10-16 01:50:07 -0400 (Wed, 16 Oct 2019)

EndedAt: 2019-10-16 01:52:32 -0400 (Wed, 16 Oct 2019)

EllapsedTime: 145.0 seconds

RetCode: 0

Status:  OK

CheckDir: genefu.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:genefu.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings genefu_2.16.0.tar.gz
###
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck’
* using R version 3.6.1 (2019-07-05)
* using platform: x86_64-pc-linux-gnu (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 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
  ‘/home/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck/00check.log’
for details.

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### Running command:
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###   /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD INSTALL genefu
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/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	0.191	0.004	0.195
boxplotplus2	0.008	0.000	0.009
claudinLow	0.828	0.000	0.828
claudinLowData	0.02	0.00	0.02
compare.proto.cor	0.864	0.008	0.872
compute.pairw.cor.meta	1.033	0.020	1.052
compute.proto.cor.meta	0.909	0.012	0.921
cordiff.dep	0.011	0.004	0.016
endoPredict	0.022	0.000	0.022
expos	0.002	0.000	0.002
fuzzy.ttest	0.001	0.000	0.001
gene70	0.163	0.000	0.163
gene76	0.042	0.000	0.042
geneid.map	0.087	0.000	0.086
genius	0.223	0.004	0.228
ggi	0.078	0.000	0.079
ihc4	0.008	0.000	0.009
intrinsic.cluster	0.309	0.000	0.285
intrinsic.cluster.predict	0.188	0.000	0.188
map.datasets	0.945	0.004	0.950
mod1	0.000	0.002	0.002
mod2	0.000	0.002	0.002
modelOvcAngiogenic	0.001	0.002	0.003
molecular.subtyping	2.736	0.032	2.902
nkis	0.001	0.000	0.002
npi	0.000	0.004	0.005
oncotypedx	0.054	0.000	0.054
ovcAngiogenic	0.066	0.004	0.070
ovcCrijns	0.068	0.000	0.067
ovcTCGA	0.19	0.00	0.19
ovcYoshihara	0.063	0.004	0.066
pam50	0.018	0.000	0.018
pik3cags	0.051	0.000	0.051
power.cor	0.000	0.000	0.001
ps.cluster	0.337	0.000	0.315
read.m.file	0.016	0.004	0.032
rename.duplicate	0.002	0.000	0.001
rescale	0.036	0.000	0.036
rorS	0.113	0.000	0.113
scmgene.robust	0.000	0.004	0.004
scmod1.robust	0.003	0.004	0.006
scmod2.robust	0.006	0.000	0.006
setcolclass.df	0.001	0.000	0.001
sig.endoPredict	0.003	0.000	0.003
sig.gene70	0.000	0.004	0.005
sig.gene76	0.004	0.000	0.004
sig.genius	0.019	0.000	0.018
sig.ggi	0.005	0.000	0.005
sig.oncotypedx	0.003	0.000	0.002
sig.pik3cags	0.003	0.000	0.003
sig.score	0.068	0.000	0.068
sig.tamr13	0.001	0.002	0.004
sigOvcAngiogenic	0.005	0.001	0.006
sigOvcCrijns	0.004	0.000	0.005
sigOvcSpentzos	0.004	0.000	0.004
sigOvcTCGA	0.005	0.000	0.005
sigOvcYoshihara	0.004	0.000	0.004
spearmanCI	0	0	0
ssp2003	0.022	0.004	0.026
ssp2006	0.023	0.008	0.031
st.gallen	0.005	0.000	0.005
stab.fs	0.094	0.000	0.094
stab.fs.ranking	0.581	0.028	0.609
strescR	0	0	0
subtype.cluster	0.413	0.000	0.412
subtype.cluster.predict	0.11	0.00	0.11
tamr13	0.034	0.008	0.042
tbrm	0	0	0
vdxs	0.000	0.001	0.001
weighted.meanvar	0.000	0.001	0.001
write.m.file	0.000	0.001	0.001