Error in re-building vignettes:
  ...

Error: processing vignette 'vignette.Rnw' failed with diagnostics:
 chunk 1 
Error : 1: Unknown IO error2: failed to load external entity "http://waterservices.usgs.gov/nwis/dv?site=05054000&parameterCd=00060&statCd=00003&startDt=2000-01-01&endDt=2010-12-31"

Execution halted
WDI: no visible binding for global variable 'WDI_data'
WDIcache: no visible global function definition for 'fromJSON'
WDIsearch: no visible binding for global variable 'WDI_data'
Packages required but not available: 'subprocess' 'semver'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
getStationCode: no visible binding for global variable
  'USAirportWeatherStations'
getStationCode: no visible binding for global variable 'IntlWxStations'
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

[1] "Welcome to the webvis pacakge."
pairtest: no visible global function definition for 'p.value'
pairtest: no visible global function definition for 'single.snp.tests'
fun.load.hals.a: no visible global function definition for 'sfExport'
fun.load.hals.a: no visible global function definition for 'sfLibrary'
fun.load.hals.fill: no visible global function definition for
  'sfExport'
fun.load.hals.fill: no visible global function definition for
  'sfLibrary'
fun.load.widals.a: no visible global function definition for 'sfExport'
fun.load.widals.a: no visible global function definition for
  'sfLibrary'
fun.load.widals.fill: no visible global function definition for
  'sfExport'
fun.load.widals.fill: no visible global function definition for
  'sfLibrary'
screen.ttest: no visible global function definition for 'colttests'
widenet: no visible global function definition for 'mc.reset.stream'
widenet: no visible global function definition for 'mclapply'
Bundesliga.Mannschaft: no visible binding for global variable
  'Bundesliga'
Bundesliga.Tabelle: no visible binding for global variable 'Bundesliga'
Bundesliga.XML: no visible binding for global variable 'Bundesliga'
Running examples in 'wiqid-Ex.R' failed
The error most likely occurred in:

> ### Name: dippers
> ### Title: Capture-recapture data for European dippers
> ### Aliases: dippers
> ### Keywords: datasets
> 
> ### ** Examples
> 
> data(dippers)
> 
> DH <- dippers[1:7]  # Extract the detection histories
> survCJS(DH)  # the phi(.) p(.) model
Call: survCJS(DH = DH)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.5602 0.5105 0.6088
p1   0.9026 0.8305 0.9460

AIC: 670.8377 
> survCJS(DH, phi ~ .time)  # the phi(t) p(.) model
Call: survCJS(DH = DH, model = phi ~ .time)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6258 0.3965 0.8098
phi2 0.4542 0.3295 0.5849
phi3 0.4784 0.3669 0.5921
phi4 0.6244 0.5079 0.7281
phi5 0.6079 0.4970 0.7088
phi6 0.5833 0.4688 0.6895
p1   0.9021 0.8286 0.9461

AIC: 673.7301 
> 
> # Floods affected the 2nd and 3rd intervals
> df <- data.frame(flood = c(FALSE, TRUE, TRUE, FALSE, FALSE, FALSE))
> survCJS(DH, phi ~ flood, data=df)
Call: survCJS(DH = DH, model = phi ~ flood, data = df)

Real values (duplicates omitted):
        est  lowCI  uppCI
phi1 0.6071 0.5451 0.6658
phi2 0.4688 0.3858 0.5537
p1   0.8998 0.8262 0.9443

AIC: 666.1028 
> 
> # Including a grouping factor:
> survCJS(DH, phi ~ flood * group, data=df, group=dippers$sex)
Call: survCJS(DH = DH, model = phi ~ flood * group, data = df, group = dippers$sex)

Real values (duplicates omitted):
          est  lowCI  uppCI
F:phi1 0.6033 0.5163 0.6842
F:phi2 0.4568 0.3468 0.5712
M:phi1 0.6108 0.5246 0.6906
M:phi2 0.4833 0.3612 0.6073
F:p1   0.8999 0.8263 0.9444

AIC: 669.9911 
> 
> # Bayesian estimation:
> 
> Bdip <- BsurvCJS(DH, parallel=FALSE)
Error: The 'rjags' package and the JAGS program are needed to run this function.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    5.0Mb
    libs   1.4Mb
Namespace in Imports field not imported from: 'RMySQL'
  All declared Imports should be used.
wordcloud: no visible global function definition for 'Corpus'
wordcloud: no visible global function definition for 'VectorSource'
wordcloud: no visible global function definition for 'tm_map'
wordcloud: no visible binding for global variable 'removePunctuation'
wordcloud : <anonymous>: no visible global function definition for
  'removeWords'
wordcloud : <anonymous>: no visible global function definition for
  'stopwords'
wordcloud: no visible global function definition for
  'TermDocumentMatrix'
wordmatch: no visible global function definition for 'llply'
wordmatch : <anonymous>: no visible global function definition for
  'llply'
wordmatch: no visible global function definition for 'melt'
wordmatch: no visible global function definition for 'count'
simul.wsvm: no visible binding for global variable 'mixture.example'
plot,x12Batch : .local: no visible binding for global variable 'xb'
x12,ts : .local: no visible binding for global variable 'out'
x12,x12Batch : .local: no visible global function definition for
  'mclapply'
x12,x12Single : .local: no visible binding for global variable 'out'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.2/xgboost.Rcheck/00install.out' for details.
R5.value.default: no visible binding for global variable 'data.table'
R5.value.default: no visible global function definition for
  'as.data.table'
R5.value.parse: no visible binding for global variable 'data.table'
R5.value.parse: no visible global function definition for
  'is.data.table'
R5.value.parse: no visible global function definition for
  'as.data.table'
File 'xml2/libs/i386/xml2.dll':
  Found non-API call to R: 'getConnection'
File 'xml2/libs/x64/xml2.dll':
  Found non-API call to R: 'getConnection'

Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.1Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile : .local: possible error in updateIds(doc, save = x):
  unused argument (save = x)
as.xts.ts: no visible global function definition for 'as.yearqtr'
as.xts.ts: no visible global function definition for 'as.yearmon'
rollapply.xts: no visible global function definition for 'na.fill'
NB: .First.lib is obsolete and will not be used in R >= 3.0.0
File 'yacca/R/zzz.R':
  .First.lib calls:
    cat(paste("'", ehelp[4], "'\n", "Version ", ehelp[2], " created on ",     ehelp[3], ".\n", sep = ""))
    cat(paste(substring(ehelp[3], first = 16), "\n", "Version ",     substring(ehelp[4], first = 16), " created on ", substring(ehelp[5],         first = 16), ".\n", sep = ""))
    cat("Copyright (c) 2008, Carter T. Butts, University of California-Irvine\n")
    cat("For citation information, type citation(\"yacca\").\n")
    cat("Type help(\"yacca-package\") to get started.\n")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.
tZC_NS: no visible global function definition for 'cmpfun'
tZC_NS_extra: no visible global function definition for 'cmpfun'
tZC_SV: no visible global function definition for 'cmpfun'
tZC_SV_extra: no visible global function definition for 'cmpfun'
epirice.weather: no visible binding for global variable
  'weather_SouthAsia'
maize.multisy: no visible binding for global variable
  'weather_EuropeEU'
maize.multisy240 : <anonymous>: no visible binding for global variable
  'weather_EuropeEU'
maize.weather: no visible binding for global variable
  'weather_FranceWest'
param.rtriangle: no visible global function definition for 'rtriangle'
population.age.model.ode: no visible global function definition for
  'ode'
population.age.model.ode: no visible global function definition for
  'rkMethod'
predator.prey.model: no visible global function definition for 'ode'
predator.prey.model: no visible global function definition for
  'rkMethod'
watbal.weather: no visible binding for global variable
  'weather_FranceWest'
Namespaces in Imports field not imported from:
  'dplyr' 'ggplot2' 'lubridate'
  All declared Imports should be used.