R Development Page

pandemic log file (check_x86_64_linux)

Fri Apr  6 17:48:31 2018: Checking package pandemic (SVN revision 1977) ...
* using log directory ‘/srv/rf/building/build_2018-04-06-18-44/RF_PKG_CHECK/PKGS/pandemic.Rcheck’
* using R version 3.5.0 alpha (2018-04-05 r74541)
* using platform: x86_64-pc-linux-gnu (64-bit)
* using session charset: UTF-8
* using option ‘--as-cran’
* checking for file ‘pandemic/DESCRIPTION’ ... OK
* checking extension type ... Package
* this is package ‘pandemic’ version ‘0.3’
* checking CRAN incoming feasibility ... NOTE
Maintainer: ‘Patrick Brown ’

New submission

The Title field should be in title case, current version then in title case:
‘Bayesian inference for data from the initial stages of a pandemic’
‘Bayesian Inference for Data from the Initial Stages of a Pandemic’

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 executable files ... OK
* checking for hidden files and directories ... OK
* checking for portable file names ... OK
* checking for sufficient/correct file permissions ... OK
* checking serialization versions ... OK
* checking whether package ‘pandemic’ can be installed ... [7s/7s] OK
* checking installed package size ... OK
* checking package directory ... OK
* checking DESCRIPTION meta-information ... OK
* checking top-level files ... NOTE
Non-standard file/directory found at top level:
  ‘test’
* 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 use of S3 registration ... OK
* checking dependencies in R code ... NOTE
Packages in Depends field not imported from:
  ‘DPpackage’ ‘ellipse’
  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 ... [11s/11s] NOTE
InfectionUnobserved: no visible global function definition for ‘rpois’
censorweibull: no visible global function definition for ‘rweibull’
dataAugment: no visible global function definition for ‘approx’
dataAugment: no visible global function definition for ‘rbinom’
dataAugment: no visible global function definition for ‘rweibull’
dweibullRound: no visible global function definition for ‘pweibull’
dweibullzero: no visible global function definition for ‘pweibull’
lostUpdate: no visible global function definition for ‘rbeta’
mcmc2: no visible global function definition for ‘rgamma’
mcmc2: no visible global function definition for ‘runif’
mcmc3: no visible global function definition for ‘runif’
mcmcInfection: no visible global function definition for ‘dpois’
mcmcInfection: no visible global function definition for ‘runif’
mcmcInfection: no visible global function definition for ‘rnorm’
mcmcInfection: no visible global function definition for ‘dgamma’
paramUpdate: no visible global function definition for ‘rnorm’
paramUpdate: no visible global function definition for ‘runif’
paramUpdateInfection: no visible global function definition for ‘rnorm’
paramUpdateInfection: no visible global function definition for ‘runif’
plotAgeProbs: no visible binding for global variable ‘quantile’
plotAgeProbs: no visible global function definition for ‘matplot’
plotAgeProbs: no visible global function definition for ‘matlines’
plotHospitals: no visible global function definition for ‘plot’
plotHospitals: no visible global function definition for ‘polygon’
plotHospitals: no visible global function definition for ‘lines’
plotPrior: no visible global function definition for ‘par’
plotPrior: no visible global function definition for ‘pdf’
plotPrior: no visible global function definition for ‘plot’
plotPrior: no visible global function definition for ‘hist’
plotPrior: no visible global function definition for ‘lines’
plotPrior: no visible global function definition for ‘dev.off’
plotPrior: no visible global function definition for ‘ellipse’
plotPrior: no visible global function definition for ‘var’
plotPrior: no visible global function definition for ‘matplot’
plotPrior: no visible global function definition for ‘quantile’
plotTotalCases: no visible global function definition for ‘matplot’
plotTotalCases: no visible global function definition for ‘lines’
plotTotalCases : : no visible global function definition for
  ‘quantile’
plotTotalCases: no visible global function definition for ‘legend’
plotUnobservedCases: no visible global function definition for
  ‘matplot’
plotUnobservedCases: no visible global function definition for ‘lines’
plotUnobservedCases : : no visible global function
  definition for ‘quantile’
plotUnobservedCases: no visible global function definition for ‘legend’
probSumWeibulls: no visible global function definition for ‘rweibull’
probsUpdate: no visible global function definition for ‘rbeta’
pweibullRound: no visible global function definition for ‘pweibull’
readPrior: no visible global function definition for ‘read.table’
rweibullRound: no visible global function definition for ‘rweibull’
sampleProbs: no visible global function definition for ‘rbeta’
simEpidemic: no visible global function definition for ‘rpois’
simEpidemic: no visible global function definition for ‘approx’
simEpidemic: no visible global function definition for ‘rbinom’
simEpidemic: no visible global function definition for ‘rweibull’
simEpidemicInfection: no visible global function definition for ‘rpois’
simEpidemicInfection: no visible global function definition for
  ‘rweibull’
simEpidemicInfection: no visible global function definition for
  ‘rbinom’
simHospitals : : no visible global function definition for
  ‘quantile’
simUnobservedInfections: no visible global function definition for
  ‘rpois’
simWeibullzero: no visible global function definition for ‘runif’
updateBinomialPoisson: no visible global function definition for
  ‘rpois’
updateBinomialPoisson: no visible global function definition for
  ‘dbinom’
updateBinomialPoisson: no visible global function definition for
  ‘dpois’
updateBinomialPoisson: no visible global function definition for
  ‘ppois’
updateBinomialPoisson: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  approx dbinom dev.off dgamma dpois ellipse hist legend lines matlines
  matplot par pdf plot polygon ppois pweibull quantile rbeta rbinom
  read.table rgamma rnorm rpois runif rweibull var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "hist", "legend", "lines", "matlines",
             "matplot", "par", "plot", "polygon")
  importFrom("stats", "approx", "dbinom", "dgamma", "dpois", "ppois",
             "pweibull", "quantile", "rbeta", "rbinom", "rgamma",
             "rnorm", "rpois", "runif", "rweibull", "var")
  importFrom("utils", "read.table")
to your NAMESPACE file.
* checking Rd files ... NOTE
prepare_Rd: mcmcPandemic.Rd:49: Dropping empty section \keyword
prepare_Rd: mcmcPandemic.Rd:50: Dropping empty section \keyword
prepare_Rd: mcmcPandemic.Rd:23-25: Dropping empty section \details
prepare_Rd: mcmcPandemic.Rd:26-28: Dropping empty section \value
prepare_Rd: mcmcPandemic.Rd:35-37: Dropping empty section \note
prepare_Rd: mcmcPandemic.Rd:29-31: Dropping empty section \references
prepare_Rd: mcmcPandemic.Rd:41-43: Dropping empty section \seealso
prepare_Rd: mcmcPandemic.Rd:44-46: Dropping empty section \examples
prepare_Rd: pandemicParams.Rd:60: Dropping empty section \keyword
prepare_Rd: pandemicParams.Rd:61: Dropping empty section \keyword
prepare_Rd: pandemicParams.Rd:40-42: Dropping empty section \note
prepare_Rd: pandemicParams.Rd:35-36: Dropping empty section \references
prepare_Rd: pandemicPriors.Rd:54: Dropping empty section \keyword
prepare_Rd: pandemicPriors.Rd:55: Dropping empty section \keyword
prepare_Rd: pandemicPriors.Rd:40-42: Dropping empty section \note
prepare_Rd: pandemicPriors.Rd:34-36: Dropping empty section \references
prepare_Rd: pandemicPriors.Rd:46-48: Dropping empty section \seealso
prepare_Rd: pandemicPriors.Rd:49-51: Dropping empty section \examples
prepare_Rd: plotPrior.Rd:48: Dropping empty section \keyword
prepare_Rd: plotPrior.Rd:49: Dropping empty section \keyword
prepare_Rd: plotPrior.Rd:23-25: Dropping empty section \details
prepare_Rd: plotPrior.Rd:26-28: Dropping empty section \value
prepare_Rd: plotPrior.Rd:35-37: Dropping empty section \note
prepare_Rd: plotPrior.Rd:29-31: Dropping empty section \references
prepare_Rd: plotPrior.Rd:40-42: Dropping empty section \seealso
prepare_Rd: plotPrior.Rd:43-45: Dropping empty section \examples
prepare_Rd: simEpidemic.Rd:49: Dropping empty section \keyword
prepare_Rd: simEpidemic.Rd:50: Dropping empty section \keyword
prepare_Rd: simEpidemic.Rd:21-23: Dropping empty section \details
prepare_Rd: simEpidemic.Rd:24-26: Dropping empty section \value
prepare_Rd: simEpidemic.Rd:33-35: Dropping empty section \note
prepare_Rd: simEpidemic.Rd:27-29: Dropping empty section \references
prepare_Rd: simEpidemic.Rd:39-41: Dropping empty section \seealso
prepare_Rd: simHospitals.Rd:45: Dropping empty section \keyword
prepare_Rd: simHospitals.Rd:46: Dropping empty section \keyword
prepare_Rd: simHospitals.Rd:20-22: Dropping empty section \details
prepare_Rd: simHospitals.Rd:23-25: Dropping empty section \value
prepare_Rd: simHospitals.Rd:32-34: Dropping empty section \note
prepare_Rd: simHospitals.Rd:26-28: Dropping empty section \references
prepare_Rd: simHospitals.Rd:38-39: Dropping empty section \seealso
prepare_Rd: simHospitals.Rd:40-42: Dropping empty section \examples
* checking Rd metadata ... OK
* checking Rd line widths ... NOTE
Rd file 'pandemicParams.Rd':
  \usage lines wider than 90 characters:
     pandemicParams(InfOns = c(mean = 1, shape = 1, zeros = 0.1), OnsMedM = c(mean = 3, shape = 2, zeros = 0.1), OnsMedS = c(mean = 2.5, sha ... [TRUNCATED]

Rd file 'pandemicPriors.Rd':
  \usage lines wider than 90 characters:
     pandemicPriors(InfOns = meanShapeZerosPrior(), OnsMedM = meanShapeZerosPrior(), OnsMedS = meanShapeZerosPrior(), OnsMedD = meanShapeZer ... [TRUNCATED]

Rd file 'plotPrior.Rd':
  \usage lines wider than 90 characters:
     plotPrior(x, posteriorSample = NULL, file = NULL, quantiles = c(0.025, 0.975), tex = FALSE, transition = NULL)

These lines will be truncated in the PDF manual.
* checking Rd cross-references ... WARNING
Unknown package ‘addAgeProbs’ in Rd xrefs
* checking for missing documentation entries ... OK
* checking for code/documentation mismatches ... OK
* checking Rd \usage sections ... WARNING
Assignments in \usage in documentation object 'readPrior':
  x = readPrior(file = "priors.txt")

Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
* checking Rd contents ... OK
* checking for unstated dependencies in examples ... OK
* checking examples ... ERROR
Running examples in ‘pandemic-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: psProbPriors
> ### Title: Priors for PSgam
> ### Aliases: psProbPriors psPrior
> 
> ### ** Examples
> 
> priors= pandemicPriors(probs=psProbPriors(hosp=psPrior(tau1=1)))
Error in psPrior(tau1 = 1) : unused argument (tau1 = 1)
Calls: pandemicPriors -> get -> psProbPriors
Execution halted
* checking PDF version of manual ... OK
* DONE

Status: 1 ERROR, 2 WARNINGs, 6 NOTEs
See
  ‘/srv/rf/building/build_2018-04-06-18-44/RF_PKG_CHECK/PKGS/pandemic.Rcheck/00check.log’
for details.

Run time: 62.5 seconds.