Package: genefu

Version: 2.15.0

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_2.15.0.tar.gz

StartedAt: 2019-04-09 00:42:12 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 00:44:33 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 141.1 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_2.15.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/genefu.Rcheck’
* using R Under development (unstable) (2019-03-18 r76245)
* 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 ‘2.15.0’
* 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 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	0.153	0.008	0.161
boxplotplus2	0.007	0.000	0.007
claudinLow	0.754	0.004	0.758
claudinLowData	0.027	0.004	0.031
compare.proto.cor	0.977	0.004	0.981
compute.pairw.cor.meta	1.260	0.004	1.263
compute.proto.cor.meta	0.856	0.012	0.868
cordiff.dep	0.015	0.000	0.015
endoPredict	0.018	0.004	0.022
expos	0.002	0.000	0.002
fuzzy.ttest	0.001	0.000	0.001
gene70	0.154	0.000	0.154
gene76	0.041	0.000	0.041
geneid.map	0.084	0.000	0.084
genius	0.208	0.012	0.220
ggi	0.079	0.000	0.079
ihc4	0.009	0.000	0.009
intrinsic.cluster	0.311	0.008	0.296
intrinsic.cluster.predict	0.203	0.000	0.204
map.datasets	0.909	0.004	0.912
mod1	0.002	0.000	0.002
mod2	0.001	0.000	0.002
modelOvcAngiogenic	0.002	0.000	0.003
molecular.subtyping	2.818	0.016	2.891
nkis	0.000	0.002	0.002
npi	0.002	0.005	0.007
oncotypedx	0.078	0.004	0.082
ovcAngiogenic	0.098	0.003	0.102
ovcCrijns	0.078	0.000	0.078
ovcTCGA	0.203	0.000	0.203
ovcYoshihara	0.074	0.004	0.079
pam50	0.021	0.004	0.025
pik3cags	0.066	0.004	0.070
power.cor	0	0	0
ps.cluster	0.468	0.004	0.453
read.m.file	0.027	0.004	0.130
rename.duplicate	0.000	0.002	0.001
rescale	0.064	0.006	0.070
rorS	0.127	0.004	0.130
scmgene.robust	0.006	0.000	0.007
scmod1.robust	0.009	0.000	0.008
scmod2.robust	0.008	0.000	0.007
setcolclass.df	0.002	0.000	0.002
sig.endoPredict	0.005	0.000	0.005
sig.gene70	0.002	0.004	0.005
sig.gene76	0.006	0.000	0.006
sig.genius	0.018	0.011	0.030
sig.ggi	0.005	0.000	0.005
sig.oncotypedx	0.003	0.000	0.003
sig.pik3cags	0.004	0.000	0.004
sig.score	0.069	0.000	0.069
sig.tamr13	0.004	0.000	0.005
sigOvcAngiogenic	0.006	0.000	0.005
sigOvcCrijns	0.005	0.000	0.004
sigOvcSpentzos	0.001	0.004	0.004
sigOvcTCGA	0.017	0.003	0.021
sigOvcYoshihara	0.005	0.000	0.005
spearmanCI	0.001	0.000	0.001
ssp2003	0.023	0.004	0.026
ssp2006	0.038	0.000	0.037
st.gallen	0.006	0.000	0.006
stab.fs	0.084	0.000	0.084
stab.fs.ranking	0.685	0.040	0.725
strescR	0.001	0.000	0.001
subtype.cluster	0.386	0.004	0.390
subtype.cluster.predict	0.112	0.004	0.116
tamr13	0.040	0.000	0.039
tbrm	0.001	0.000	0.000
vdxs	0.002	0.000	0.001
weighted.meanvar	0.001	0.000	0.000
write.m.file	0.002	0.000	0.001