Package: iterativeBMAsurv

Version: 1.41.0

Command: /home/biocbuild/bbs-3.9-bioc/R/bin/R CMD check --install=check:iterativeBMAsurv.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iterativeBMAsurv_1.41.0.tar.gz

StartedAt: 2019-04-09 01:29:28 -0400 (Tue, 09 Apr 2019)

EndedAt: 2019-04-09 01:31:08 -0400 (Tue, 09 Apr 2019)

EllapsedTime: 100.6 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMAsurv.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:iterativeBMAsurv.install-out.txt --library=/home/biocbuild/bbs-3.9-bioc/R/library --no-vignettes --timings iterativeBMAsurv_1.41.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.9-bioc/meat/iterativeBMAsurv.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 ‘iterativeBMAsurv/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘iterativeBMAsurv’ version ‘1.41.0’
* checking package namespace information ... OK
* checking package dependencies ... OK
* 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 ‘iterativeBMAsurv’ can be installed ... OK
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘survival’
A package should be listed in only one of these fields.
* 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
Packages in Depends field not imported from:
  ‘BMA’ ‘leaps’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
iterateBMAsurv.train: no visible global function definition for
  ‘bic.surv’
iterateBMAsurv.train.wrapper: no visible global function definition for
  ‘bic.surv’
Undefined global functions or variables:
  bic.surv
* checking Rd files ... NOTE
prepare_Rd: predictBicSurv.Rd:46: Dropping empty section \note
prepare_Rd: predictiveAssessCategory.Rd:52: Dropping empty section \note
prepare_Rd: printTopGenes.Rd:49: Dropping empty section \note
prepare_Rd: singleGeneCoxph.Rd:54: Dropping empty section \note
prepare_Rd: testCens.Rd:13-14: Dropping empty section \details
prepare_Rd: testSurv.Rd:13-14: Dropping empty section \details
prepare_Rd: trainCens.Rd:13-14: Dropping empty section \details
prepare_Rd: trainSurv.Rd:13-14: Dropping empty section \details
* checking Rd metadata ... OK
* checking Rd cross-references ... OK
* 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
Examples with CPU or elapsed time > 5s
                               user system elapsed
imageplot.iterate.bma.surv   13.645  0.000  13.650
iterateBMAsurv.train          8.549  0.015   8.567
predictiveAssessCategory      7.570  0.040   7.615
iterateBMAsurv.train.wrapper  7.157  0.000   7.162
predictBicSurv                6.317  0.016   6.343
* 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: 4 NOTEs
See
  ‘/home/biocbuild/bbs-3.9-bioc/meat/iterativeBMAsurv.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 iterativeBMAsurv
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* installing to library ‘/home/biocbuild/bbs-3.9-bioc/R/library’
* installing *source* package ‘iterativeBMAsurv’ ...
** using staged installation
** R
** data
** 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 (iterativeBMAsurv)

name	user	system	elapsed
crossVal	2.164	0.004	2.176
imageplot.iterate.bma.surv	13.645	0.000	13.650
iterateBMAsurv.train	8.549	0.015	8.567
iterateBMAsurv.train.predict.assess	0.926	0.017	0.942
iterateBMAsurv.train.wrapper	7.157	0.000	7.162
iterativeBMAsurv-package	2.501	0.019	2.522
predictBicSurv	6.317	0.016	6.343
predictiveAssessCategory	7.570	0.040	7.615
printTopGenes	0.448	0.000	0.449
singleGeneCoxph	0.365	0.000	0.366