Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
negative edges length changed to 0!
Quitting from lines 115-133 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/treespace.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

   /// adegenet 2.1.1 is loaded ////////////

   > overview: '?adegenet'
   > tutorials/doc/questions: 'adegenetWeb()' 
   > bug reports/feature requests: adegenetIssues()



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
Running examples in ‘tricolore-Ex.R’ failed
The error most likely occurred in:

> ### Name: ColorKey
> ### Title: Ternary Balance Scheme Legend
> ### Aliases: ColorKey
> ### Keywords: internal
> 
> ### ** Examples
> 
> tricolore:::ColorKey(breaks = 5, h_ = 0, c_ = 140, l_ = 70, contrast = 0.5,
+                      center = rep(1/3, 3), spread = 1)
Error in (function (el, elname)  : 
  "plot.tag" is not a valid theme element name.
Calls: <Anonymous> ... update_theme -> do.call -> <Anonymous> -> mapply -> <Anonymous>
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                 stop("Element ", elname, " must be a unit vector of length 4.")
         }
         else if (!inherits(el, eldef$class) && !inherits(el, "element_blank")) {
             stop("Element ", elname, " must be a ", eldef$class, " object.")
         }
         invisible()
     })(dots[[1L]][[50L]], dots[[2L]][[50L]])
  10: stop("\"", elname, "\" is not a valid theme element name.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 33 SKIPPED: 0 FAILED: 1
  1. Error: NA, Inf, NaNs in input return NA in output (@test-global.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-42 (european_education.Rmd) 
Error: processing vignette 'european_education.Rmd' failed with diagnostics:
"plot.tag" is not a valid theme element name.
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-71 (trip.Rmd) 
Error: processing vignette 'trip.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qexpfamily.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.35 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Packages suggested but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’ ‘RPostgreSQL’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSPostgreSQL’, ‘TSodbc’, ‘RPostgreSQL’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxXmlContentException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

> user <- Sys.getenv("MYSQL_USER")

> setup <- RMySQL::dbConnect(RMySQL::MySQL(), dbname = "test")

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Error in re-building vignettes:
  ...
Error: processing vignette 'tsdisagg2manual.ltx' failed with diagnostics:
Running 'texi2dvi' on 'tsdisagg2manual.ltx' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.

WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot43b24adea0a5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot43b24adea0a5.png': No such file or directory
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘tuneRanger-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimateTimeTuneRanger
> ### Title: estimateTimeTuneRanger
> ### Aliases: estimateTimeTuneRanger
> 
> ### ** Examples
> 
> estimateTimeTuneRanger(iris.task)
Error in setHyperPars2.Learner(learner, insert(par.vals, args)) : 
  order is not feasible for parameter 'respect.unordered.factors'!
Calls: estimateTimeTuneRanger ... setHyperPars -> setHyperPars2 -> setHyperPars2.Learner
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Error: classification ranger (@test_base.R#15)  ──────────────────────────
  order is not feasible for parameter 'respect.unordered.factors'!
  1: estimateTimeTuneRanger(iris.task, num.trees = 100, num.threads = 1) at testthat/test_base.R:15
  2: makeLearner(paste0(type, ".ranger"), par.vals = par.vals, predict.type = predict.type)
  3: setHyperPars(learner = wl, ..., par.vals = par.vals)
  4: setHyperPars2(learner, insert(par.vals, args))
  5: setHyperPars2.Learner(learner, insert(par.vals, args))
  6: stop(msg)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: classification ranger (@test_base.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘survey’

The following object is masked from ‘package:graphics’:

    dotchart

Loading required package: xtable
Loading required package: latticeExtra
Loading required package: RColorBrewer
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'iptw.tex' failed.
LaTeX errors:
! LaTeX Error: File `srcltx.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       21.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'design.tex' failed.
LaTeX errors:
! LaTeX Error: File `apalike.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
umxConfint: no visible global function definition for ‘omxRunCI’
Undefined global functions or variables:
  omxRunCI
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: residuals.MxModel
> ### Title: Get residuals from an MxModel
> ### Aliases: residuals.MxModel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> latents  = c("g")
> manifests = names(demoOneFactor)
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: umxRun -> mxRun -> runHelper
Execution halted
Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: message(e)
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_umx_has_CI.r#41) 
  2. Error: (unknown) (@test_umx_is_RAM.r#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: reshape
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cap-recap.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 126-127 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                	      <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning: 'data' shows efficiency > 1; this looks almost too good to be true
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usl.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [scaled=0.85]{beramono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.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.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
'library' or 'require' call to ‘foreach’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for ‘pexp’
ll.coverage.optim.const.post.9m: no visible global function definition
  for ‘dexp’
make.sample.pop: no visible global function definition for ‘runif’
mcmc.converge: no visible global function definition for ‘par’
mcmc.converge: no visible global function definition for ‘plot’
mcmc.converge: no visible global function definition for ‘points’
mcmc.converge: no visible global function definition for ‘density’
mcmc.converge: no visible global function definition for ‘lines’
mcmc.converge : <anonymous>: no visible global function definition for
  ‘sd’
mcmc.estimate : run.chain: no visible global function definition for
  ‘dexp’
mcmc.estimate : run.chain: no visible global function definition for
  ‘rnorm’
mcmc.estimate : run.chain: no visible global function definition for
  ‘runif’
mcmc.estimate : run.chain: no visible global function definition for
  ‘par’
mcmc.estimate : run.chain: no visible global function definition for
  ‘plot’
mcmc.estimate: no visible global function definition for ‘%dopar%’
mcmc.estimate: no visible global function definition for ‘foreach’
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for ‘runif’
vaccinate.sample.pop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘coverageTest.r’ [0s/1s]
Running the tests in ‘tests/coverageTest.r’ failed.
Last 13 lines of output:
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in getTestPaths("vacem", "tests/testUtils.r") : 
    could not find function "getTestPaths"
  Calls: source
  Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘devtools’
Missing or unexported object: ‘validate::%vin%’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/VBmix.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Package required and available but unsuitable version: ‘webmockr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vdg.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.75 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Error in re-building vignettes:
  ...

The following object is masked from ‘package:base’:

    backsolve

Loading required package: grid
Warning in structure(ia, dimnames = NULL) :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ConfoundingPotential.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {keyval}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.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.
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  49.1Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'walkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/wand.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/warbleR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
There are  2000 missing values for 05054000 or 49.78 percent of the data.
The maximum block of missing 05054000 data is 12 days long.
Filled in 2000 values for 05054000
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Watersheds.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.14 \bibliographystyle
                       {apacite}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org/data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WebGestaltR.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: def)

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test-all.R’ [2s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > test_check("webmockr")
  Loading required package: webmockr
  ── 1. Error: (unknown) (@test-no-cassette-in-use.R#3)  ─────────────────────────
  there is no package called 'vcr'
  1: library(vcr) at testthat/test-no-cassette-in-use.R:3
  2: stop(txt, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 422 SKIPPED: 7 FAILED: 1
  1. Error: (unknown) (@test-no-cassette-in-use.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rgeolocate’
Error in re-building vignettes:
  ...
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
 [>] 490 sequences with 6 distinct states
 [>] creating a 'sm' with a single substitution cost of 1
 [>] creating 6x6 substitution-cost matrix using 1 as constant value
 [>] 490 distinct sequences
 [>] min/max sequence length: 70/70
 [>] computing distances using the HAM metric
 [>] elapsed time: 0.17 secs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.78 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Definition.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  ‘org.Hs.eg.db’ ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'funwithfunload.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘genefilter’
Unexported objects imported by ':::' calls:
  ‘circular:::DensityCircularRad’ ‘circular:::DvonmisesRad’
  ‘circular:::DwrappednormalRad’ ‘circular:::MlevonmisesRad’
  ‘circular:::MlewrappednormalRad’
  See the note in ?`:::` about the use of this operator.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 218-220 (wflow-01-getting-started.Rmd) 
Error: processing vignette 'wflow-01-getting-started.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running ‘test-all.R’ [0s/0s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("worrms")
  Loading required package: worrms
  Error in library("vcr") : there is no package called 'vcr'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wrappedvig.ltx' failed with diagnostics:
Running 'texi2dvi' on 'wrappedvig.ltx' failed.
LaTeX errors:
! Package pdftex.def Error: File `wrappedv1-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv2-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv3-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv4-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
Packages suggested but not available for checking: ‘GenomicScores’ ‘ggbio’
Error in re-building vignettes:
  ...
Loading required package: Xmisc

Attaching package: ‘Xmisc’

The following object is masked from ‘package:base’:

    dir.exists

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Xmisc-ArgumentParser.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OtherPackagesGallery.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {hyperref} % hyperref last^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘MBESS’
Running examples in ‘yhat-Ex.R’ failed
The error most likely occurred in:

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Package suggested but not available for checking: ‘loon’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'zipfr-tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)

! Emergency stop.
<read *> 
         
l.13 \setpapersize
                  [portrait]{A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/zstdr.Rcheck/00install.out’ for details.