BioC 3.1: CHECK report for iterativeBMAsurv on zin2

Package: iterativeBMAsurv

Version: 1.26.0

Command: /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMAsurv_1.26.0.tar.gz

StartedAt: 2015-10-09 02:52:00 -0700 (Fri, 09 Oct 2015)

EndedAt: 2015-10-09 02:53:20 -0700 (Fri, 09 Oct 2015)

EllapsedTime: 79.9 seconds

RetCode: 0

Status:  OK

CheckDir: iterativeBMAsurv.Rcheck

Warnings: 0

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### Running command:
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###   /home/biocbuild/bbs-3.1-bioc/R/bin/R CMD check --no-vignettes --timings iterativeBMAsurv_1.26.0.tar.gz
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* using log directory ‘/home/biocbuild/bbs-3.1-bioc/meat/iterativeBMAsurv.Rcheck’
* using R version 3.2.2 (2015-08-14)
* 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 ‘1.26.0’
* 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 ... [2s/2s] 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 loading without being on the library search path ... 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’
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking installed files from ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ... [33s/45s] OK
Examples with CPU or elapsed time > 5s
                              user system elapsed
imageplot.iterate.bma.surv   9.463  0.013  13.712
predictiveAssessCategory     4.865  0.023   5.797
iterateBMAsurv.train         4.848  0.008   5.609
predictBicSurv               4.702  0.016   6.459
iterateBMAsurv.train.wrapper 4.587  0.000   6.400
* 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-3.1-bioc/meat/iterativeBMAsurv.Rcheck/00check.log’
for details.

* installing *source* package ‘iterativeBMAsurv’ ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (iterativeBMAsurv)

name	user	system	elapsed
crossVal	1.277	0.021	1.602
imageplot.iterate.bma.surv	9.463	0.013	13.712
iterateBMAsurv.train	4.848	0.008	5.609
iterateBMAsurv.train.predict.assess	0.588	0.015	0.893
iterateBMAsurv.train.wrapper	4.587	0.000	6.400
iterativeBMAsurv-package	1.806	0.000	2.836
predictBicSurv	4.702	0.016	6.459
predictiveAssessCategory	4.865	0.023	5.797
printTopGenes	0.246	0.000	0.402
singleGeneCoxph	0.244	0.000	0.370