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rcolgem log file (check_x86_64_windows)

* using log directory 'R:/run/building/build_2016-05-21-01-04/RF_PKG_CHECK/PKGS/rcolgem.Rcheck'
* using R version 3.3.0 Patched (2016-05-20 r70655)
* using platform: x86_64-w64-mingw32 (64-bit)
* using session charset: ISO8859-1
* using option '--as-cran'
* checking for file 'rcolgem/DESCRIPTION' ... OK
* checking extension type ... Package
* this is package 'rcolgem' version '0.0.5'
* checking CRAN incoming feasibility ...Warning: R:/run/building/build_2016-05-21-01-04/RF_PKG_CHECK/PKGS/rcolgem.Rcheck/00_pkg_src/rcolgem/man/phylo.source.attribution.Rd:1: All text must be in a section
 NOTE
Maintainer: 'Erik M Volz '

New submission

The Title field should be in title case, current version then in title case:
'statistical inference and modeling of genealogies generated by epidemic and ecological processes'
'Statistical Inference and Modeling of Genealogies Generated by Epidemic and Ecological Processes'

The Description field should not start with the package name,
  'This package' or similar.

The Date field is over a month old.
* 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 whether package 'rcolgem' can be installed ... WARNING
Found the following significant warnings:
  Warning: R:/run/building/build_2016-05-21-01-04/RF_PKG_CHECK/PKGS/rcolgem.Rcheck/00_pkg_src/rcolgem/man/phylo.source.attribution.Rd:1: All text must be in a section
See 'R:/run/building/build_2016-05-21-01-04/RF_PKG_CHECK/PKGS/rcolgem.Rcheck/00install.out' for details.
* checking installed package size ... OK
* 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 ... WARNING
Vignettes with missing or empty \VignetteIndexEntry:
  hiv_simtree_vignette.Rnw
  hiv_vignette.Rnw
  sir_vignette.Rnw
See sections 'The INDEX file' and 'Package subdirectories' in the
'Writing R Extensions' manual.
* checking package subdirectories ... OK
* checking R files for non-ASCII characters ... OK
* checking R files for syntax errors ... OK
* loading checks for arch 'i386'
** 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 use of S3 registration ... OK
* loading checks for arch 'x64'
** 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 use of S3 registration ... OK
* checking dependencies in R code ... WARNING
'library' or 'require' call not declared from: 'data.table'
'library' or 'require' calls to packages already attached by Depends:
  'ape' 'deSolve'
  Please remove these calls from your code.
'library' or 'require' call to 'data.table' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
* checking S3 generic/method consistency ... WARNING
solve:
  function(a, b, ...)
solve.model:
  function(t0, t1, x0, births, deaths, nonDemeDynamics, parms,
           migrations, integrationMethod, timeResolution)

solve:
  function(a, b, ...)
solve.model.unstructured:
  function(t0, t1, x0, births, deaths, nonDemeDynamics, parms,
           timeResolution, integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree:
  function(births, deaths, nonDemeDynamics, t0, x0, sampleTimes,
           sampleStates, migrations, parms, fgyResolution,
           integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree.0:
  function(births, deaths, nonDemeDynamics, t0, x0, sampleTimes,
           sampleStates, migrations, parms, fgyResolution,
           integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree.2:
  function(births, deaths, nonDemeDynamics, t0, x0, sampleTimes,
           sampleStates, migrations, parms, fgyResolution,
           integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree.fgy:
  function(times, births, migrations, demeSizes, sampleTimes,
           sampleStates, integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree.fgy.2:
  function(times, births, migrations, demeSizes, sampleTimes,
           sampleStates, integrationMethod)

simulate:
  function(object, nsim, seed, ...)
simulate.binary.dated.tree.unstructured:
  function(births, deaths, nonDemeDynamics, t0, x0, sampleTimes, parms,
           fgyResolution, integrationMethod)

See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.

Found the following apparent S3 methods exported but not registered:
  simulate.binary.dated.tree simulate.binary.dated.tree.0
  simulate.binary.dated.tree.2 simulate.binary.dated.tree.fgy
  simulate.binary.dated.tree.fgy.2
  simulate.binary.dated.tree.unstructured solve.model
  solve.model.unstructured
See section 'Registering S3 methods' in the 'Writing R Extensions'
manual.
* checking replacement functions ... OK
* checking foreign function calls ... OK
* checking R code for possible problems ... NOTE
build.demographic.process: no visible binding for '<<-' assignment to
  'Fcpp'
build.demographic.process: no visible global function definition for
  'signature'
build.demographic.process: no visible binding for '<<-' assignment to
  'Gcpp'
build.demographic.process: no visible binding for '<<-' assignment to
  'death.cpp'
build.demographic.process: no visible binding for '<<-' assignment to
  'nonDemeDynamics.cpp'
build.demographic.process: no visible binding for '<<-' assignment to
  '.dx__solve.demographic.process'
build.demographic.process : : no visible global function
  definition for 'Fcpp'
build.demographic.process : : no visible global function
  definition for 'Gcpp'
build.demographic.process : : no visible global function
  definition for 'death.cpp'
build.demographic.process : : no visible global function
  definition for 'setNames'
build.demographic.process : : no visible global function
  definition for 'nonDemeDynamics.cpp'
build.demographic.process : solve.demographic.process: no visible
  binding for global variable '.dx__solve.demographic.process'
build.demographic.process : solve.demographic.process : : no
  visible global function definition for 'Fcpp'
build.demographic.process : solve.demographic.process : : no
  visible global function definition for 'Gcpp'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'Fcpp'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'rnorm'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'Gcpp'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'death.cpp'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'nonDemeDynamics.cpp'
build.demographic.process : solve.demographic.process: no visible
  global function definition for 'setNames'
build.demographic.process : solve.demographic.process : dx: no visible
  global function definition for 'setNames'
build.demographic.process: multiple local function definitions for
  'solve.demographic.process' with different formal arguments
calculate.cluster.size.distr.from.tree : : no visible global
  function definition for 'as.data.table'
calculate.cluster.size.moments.from.model: no visible global function
  definition for 'modifyList'
calculate.cluster.size.moments.from.model: no visible binding for
  global variable 'F.'
calculate.cluster.size.moments.from.model: no visible binding for
  global variable 'G.'
calculate.cluster.size.moments.from.model: no visible binding for
  global variable 'Y.'
coalescent.log.likelihood.fgy: no visible binding for global variable
  'tfgy'
coalescent.log.likelihood.unstructuredModel : : no visible
  global function definition for 'approxfun'
make.fgy : dx: no visible global function definition for 'setNames'
phylo.source.attribution: no visible global function definition for
  'setNames'
pseudoLogLikelihood0.fgy: no visible binding for global variable 'm'
pseudoLogLikelihood0.fgy: no visible global function definition for
  'approxfun'
pseudoLogLikelihood0.fgy : objfun.ks: no visible global function
  definition for 'ks.test'
pseudoLogLikelihood0.fgy: no visible global function definition for
  'optimise'
pseudoLogLikelihood0.fgy: no visible global function definition for
  'ks.test'
show.demographic.process: no visible global function definition for
  'legend'
sim.co.tree.fgy: no visible global function definition for 'tail'
sim.co.tree.fgy : : no visible global function definition
  for 'approx'
sim.co.tree.fgy: no visible global function definition for 'approx'
sim.co.tree.fgy: no visible global function definition for 'runif'
simulate.binary.dated.tree.0: no visible global function definition for
  'runif'
simulate.binary.dated.tree.0: no visible global function definition for
  'rexp'
simulate.binary.dated.tree.fgy: no visible global function definition
  for 'coef'
simulate.binary.dated.tree.fgy: no visible global function definition
  for 'lm'
simulate.binary.dated.tree.fgy: no visible global function definition
  for 'approxfun'
simulate.binary.dated.tree.fgy: no visible global function definition
  for 'approx'
simulate.binary.dated.tree.fgy: no visible global function definition
  for 'runif'
simulate.binary.dated.tree.fgy.2: no visible global function definition
  for 'coef'
simulate.binary.dated.tree.fgy.2: no visible global function definition
  for 'lm'
simulate.binary.dated.tree.fgy.2: no visible global function definition
  for 'approxfun'
simulate.binary.dated.tree.fgy.2: no visible global function definition
  for 'approx'
simulate.binary.dated.tree.fgy.2: no visible global function definition
  for 'runif'
Undefined global functions or variables:
  .dx__solve.demographic.process F. Fcpp G. Gcpp Y. approx approxfun
  as.data.table coef death.cpp ks.test legend lm m modifyList
  nonDemeDynamics.cpp optimise rexp rnorm runif setNames signature tail
  tfgy
Consider adding
  importFrom("graphics", "legend")
  importFrom("methods", "signature")
  importFrom("stats", "approx", "approxfun", "coef", "ks.test", "lm",
             "optimise", "rexp", "rnorm", "runif", "setNames")
  importFrom("utils", "modifyList", "tail")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
* checking Rd files ... WARNING
prepare_Rd: coalescent.log.likelihood.Rd:49-51: Dropping empty section \note
prepare_Rd: phylo.source.attribution.Rd:1: All text must be in a section
prepare_Rd: phylo.source.attribution.Rd:38-40: Dropping empty section \note
prepare_Rd: phylo.source.attribution.Rd:44-45: Dropping empty section \seealso
checkRd: (5) simulate.binary.dated.tree.Rd:0-30: Must have a \description
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'phylo.source.attribution.Rd':
  \usage lines wider than 90 characters:
     phylo.source.attribution( trees, sampleTimes, f.t, Y.t, maxTMRCA = NULL, res = 1e3, treeErrorTol = 1e-3)

Rd file 'simulate.binary.dated.tree.Rd':
  \usage lines wider than 90 characters:
       simulate.binary.dated.tree(births, deaths, nonDemeDynamics,  t0, x0, sampleTimes, sampleStates,  migrations=NA,  parms=NA, fgyResolut ... [TRUNCATED]

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... OK
* checking for missing documentation entries ... WARNING
Undocumented code objects:
  'DatedTree' 'SIMULATIONTIMERESOLUTION' 'build.demographic.process'
  'calculate.cluster.size.distr.from.tree'
  'coalescent.log.likelihood.fgy' 'coalescent.log.likelihood.fgy2'
  'coalescent.log.likelihood.unstructuredModel' 'dAL' 'dCA' 'dQAL'
  'finite_size_correction' 'initfunc' 'initfunc_dCA' 'make.fgy'
  'pseudoLogLikelihood0.fgy' 'rescale.binaryDatedTree'
  'show.demographic.process' 'sim.co.tree' 'sim.co.tree.fgy'
  'simulate.binary.dated.tree.0' 'simulate.binary.dated.tree.2'
  'simulate.binary.dated.tree.fgy' 'simulate.binary.dated.tree.fgy.2'
  'simulate.binary.dated.tree.unstructured' 'simulateTreeCpp2'
  'solve.model' 'solve.model.unstructured' 'updateWCpp'
  'update_mstates_arma'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking for code/documentation mismatches ... WARNING
Codoc mismatches from documentation object 'calculate.cluster.size.moments.from.model':
calculate.cluster.size.moments.from.model
  Code: function(sampleTime, sampleStates, FGY = NULL, maxTime = NA,
                 minTime = NA, timeResolution = 50, discretizeRates =
                 FALSE, fgyResolution = 100, integrationMethod =
                 "adams")
  Docs: function(sampleTime, sampleStates, maxTime = NA, minTime = NA,
                 timeResolution = 50, discretizeRates = FALSE,
                 fgyResolution = 100, integrationMethod = "adams")
  Argument names in code not in docs:
    FGY
  Mismatches in argument names (first 3):
    Position: 3 Code: FGY Docs: maxTime
    Position: 4 Code: maxTime Docs: minTime
    Position: 5 Code: minTime Docs: timeResolution

* checking Rd \usage sections ... NOTE
S3 methods shown with full name in documentation object 'simulate.binary.dated.tree':
  'simulate.binary.dated.tree'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
* checking Rd contents ... WARNING
Argument items with no description in Rd object 'calculate.cluster.size.moments.from.model':
  'maxTime' 'minTime'

* checking for unstated dependencies in examples ... OK
* checking line endings in C/C++/Fortran sources/headers ... OK
* checking line endings in Makefiles ... OK
* checking compilation flags in Makevars ... OK
* checking for GNU extensions in Makefiles ... OK
* checking for portable use of $(BLAS_LIBS) and $(LAPACK_LIBS) ... OK
* checking compiled code ... NOTE
File 'rcolgem/libs/i386/rcolgem.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'treeSimulatorCpp2.o'
File 'rcolgem/libs/x64/rcolgem.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Object: 'treeSimulatorCpp2.o'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
* checking sizes of PDF files under 'inst/doc' ... OK
* checking installed files from 'inst/doc' ... OK
* checking files in 'vignettes' ... NOTE
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
* checking examples ... NONE
* checking for unstated dependencies in vignettes ... NOTE
'library' or 'require' calls not declared from:
  'bbmle' 'rjson'
* checking package vignettes in 'inst/doc' ... OK
* checking re-building of vignette outputs ... WARNING
Error in re-building vignettes:
  ...
Loading required package: ape
Loading required package: deSolve

Attaching package: 'deSolve'

The following object is masked from 'package:graphics':

    matplot

Loading required package: inline
Warning in if (!is.na(sampleStates)) if (!is.matrix(sampleStates)) stop("sampleStates must be a matrix (not a data.frame)") :
  the condition has length > 1 and only the first element will be used

Error: processing vignette 'hiv_vignette.Rnw' failed with diagnostics:
 chunk 10 
Error in library(bbmle) : there is no package called 'bbmle'
Execution halted

* checking PDF version of manual ... OK
* DONE

Status: 9 WARNINGs, 7 NOTEs
See
  'R:/run/building/build_2016-05-21-01-04/RF_PKG_CHECK/PKGS/rcolgem.Rcheck/00check.log'
for details.


Run time: 157.52 seconds.