Package: gaucho

Version: 1.18.0

Command: /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaucho.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaucho_1.18.0.tar.gz

StartedAt: 2019-04-16 00:03:34 -0400 (Tue, 16 Apr 2019)

EndedAt: 2019-04-16 00:04:41 -0400 (Tue, 16 Apr 2019)

EllapsedTime: 67.7 seconds

RetCode: 1

Status:  ERROR

CheckDir: gaucho.Rcheck

Warnings: NA

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD check --install=check:gaucho.install-out.txt --library=/Library/Frameworks/R.framework/Versions/Current/Resources/library --no-vignettes --timings gaucho_1.18.0.tar.gz
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* using log directory ‘/Users/biocbuild/bbs-3.8-bioc/meat/gaucho.Rcheck’
* using R version 3.5.3 (2019-03-11)
* using platform: x86_64-apple-darwin15.6.0 (64-bit)
* using session charset: UTF-8
* using option ‘--no-vignettes’
* checking for file ‘gaucho/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘gaucho’ version ‘1.18.0’
* checking package namespace information ... OK
* checking package dependencies ... NOTE
Depends: includes the non-default packages:
  ‘compiler’ ‘GA’ ‘graph’ ‘heatmap.plus’ ‘png’ ‘Rgraphviz’
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 ‘gaucho’ can be installed ... WARNING
Found the following significant warnings:
  Warning: Package 'gaucho' is deprecated and will be removed from Bioconductor
See ‘/Users/biocbuild/bbs-3.8-bioc/meat/gaucho.Rcheck/00install.out’ for details.
* checking installed package size ... OK
* checking package directory ... OK
* checking ‘build’ directory ... OK
* checking DESCRIPTION meta-information ... NOTE
Malformed Description field: should contain one or more complete sentences.
Authors@R field gives more than one person with maintainer role:
  Alex Murison <Alexander.Murison@icr.ac.uk> [aut, cre]
  Christopher Wardell <Christopher.Wardell@icr.ac.uk> [aut, cre]
* 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 ... OK
* checking S3 generic/method consistency ... OK
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
gaucho : generate_phylogeny_aware_individual: no visible global
  function definition for ‘runif’
gaucho : phylo_mutate: no visible global function definition for
  ‘runif’
gauchoReport: no visible global function definition for ‘write.table’
gauchoReport: no visible global function definition for ‘png’
gauchoReport: no visible global function definition for ‘dev.off’
gauchoReport: no visible global function definition for ‘layout’
gauchoReport: no visible global function definition for ‘par’
gauchoReport: no visible global function definition for ‘plot.new’
gauchoReport: no visible global function definition for ‘legend’
gauchoReport: no visible global function definition for ‘barplot’
gauchoReport: no visible global function definition for ‘as’
new_phylo: no visible global function definition for ‘runif’
Undefined global functions or variables:
  as barplot dev.off layout legend par plot.new png runif write.table
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "barplot", "layout", "legend", "par",
             "plot.new")
  importFrom("methods", "as")
  importFrom("stats", "runif")
  importFrom("utils", "write.table")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... OK
* 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 sizes of PDF files under ‘inst/doc’ ... OK
* checking files in ‘vignettes’ ... OK
* checking examples ...sh: line 1: 11695 Segmentation fault: 11  LANGUAGE=en _R_CHECK_INTERNALS2_=1 '/Library/Frameworks/R.framework/Resources/bin/R' --vanilla > 'gaucho-Ex.Rout' 2>&1 < gaucho-Ex.R
 ERROR
Running examples in ‘gaucho-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: gaucho
> ### Title: Genetic Algorithm for Understanding Clonal Heterogeneity and
> ###   Ordering (GAUCHO)
> ### Aliases: gaucho
> 
> ### ** Examples
> 
> ## The vignette provides far more in-depth explanation and examples ##
> 
> ## Load the included simple example data
> gaucho_simple_data = read.table(file.path(system.file("extdata",package="gaucho"),"gaucho_simple_data.txt"),header=TRUE,row.names=1)
> 
> ## Run gaucho using 3 clones and a phylogeny with a single root
> solution=gaucho(gaucho_simple_data, number_of_clones=3,nroot=1,iterations=1000)

 *** caught segfault ***
address 0x7f8e7ca1b478, cause 'memory not mapped'

Traceback:
 1: ga_tourSelection_Rcpp(object, k)
 2: selection(object)
 3: ga(type = "binary", fitness = fit_phylogeny, population = generate_phylogeny_aware_population,     selection = gabin_tourSelection, crossover = phylo_cross,     mutation = phylo_mutate, popSize = pop_size, nBits = numBits,     pmutation = mutation_rate, maxiter = iterations, elitism = parthenogenesis,     run = stoppingCriteria)
 4: gaucho(gaucho_simple_data, number_of_clones = 3, nroot = 1, iterations = 1000)
An irrecoverable exception occurred. R is aborting now ...
* 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: 1 ERROR, 1 WARNING, 3 NOTEs
See
  ‘/Users/biocbuild/bbs-3.8-bioc/meat/gaucho.Rcheck/00check.log’
for details.

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### Running command:
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###   /Library/Frameworks/R.framework/Versions/Current/Resources/bin/R CMD INSTALL gaucho
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* installing to library ‘/Library/Frameworks/R.framework/Versions/3.5/Resources/library’
* installing *source* package ‘gaucho’ ...
** R
** 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
Warning: Package 'gaucho' is deprecated and will be removed from Bioconductor
  version 3.9
* DONE (gaucho)

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