installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 110.7Mb
  sub-directories of 1Mb or more:
    doc     10.7Mb
    libs    96.2Mb
    sqlite   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Malformed Description field: should contain one or more complete sentences.
Deprecated license: BSD
Packages in Depends field not imported from:
  ‘Matrix’ ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for ‘sparseMatrix’
gmdDeflation: no visible global function definition for ‘rnorm’
laplacian: no visible global function definition for ‘sparseMatrix’
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sgt.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Various techniques are used
to find a suitable Scala installation.  Details on the search are available
using "rscala::scalaInfo(verbose=TRUE)".  Note that Scala itself requires Java.

Users can install Scala with "rscala::scalaInstall()", which places Scala in
the user's home directory under "~/.rscala".  System administrators can use
"rscala::scalaInstall(global=TRUE)", which places Scala in the package's
directory but requires a new installation every time the package is updated.
To avoid this, a conventional Scala installation can be performed as described
here: http://www.scala-lang.org/download/install.html.

Error in get(f, envir = code_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Various techniques are used
to find a suitable Scala installation.  Details on the search are available
using "rscala::scalaInfo(verbose=TRUE)".  Note that Scala itself requires Java.

Users can install Scala with "rscala::scalaInstall()", which places Scala in
the user's home directory under "~/.rscala".  System administrators can use
"rscala::scalaInstall(global=TRUE)", which places Scala in the package's
directory but requires a new installation every time the package is updated.
To avoid this, a conventional Scala installation can be performed as described
here: http://www.scala-lang.org/download/install.html.

Error in get(f, envir = code_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> -> lapply -> FUN -> get
Execution halted
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Various techniques are used
to find a suitable Scala installation.  Details on the search are available
using "rscala::scalaInfo(verbose=TRUE)".  Note that Scala itself requires Java.

Users can install Scala with "rscala::scalaInstall()", which places Scala in
the user's home directory under "~/.rscala".  System administrators can use
"rscala::scalaInstall(global=TRUE)", which places Scala in the package's
directory but requires a new installation every time the package is updated.
To avoid this, a conventional Scala installation can be performed as described
here: http://www.scala-lang.org/download/install.html.

Error in get(n, envir = env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> ... withCallingHandlers -> do.call -> <Anonymous> -> get
Execution halted
Searching for a suitable Scala installation.
  * FAILURE: 'scala.home' argument is NULL
  * FAILURE: 'rscala.scala.home' (<UNSET>) global option
  * FAILURE: SCALA_HOME () environment variable
  * FAILURE: 'scala' in the shell's search path

Cannot find a suitable Scala installation.

Scala is not distributed with the rscala package.  Various techniques are used
to find a suitable Scala installation.  Details on the search are available
using "rscala::scalaInfo(verbose=TRUE)".  Note that Scala itself requires Java.

Users can install Scala with "rscala::scalaInstall()", which places Scala in
the user's home directory under "~/.rscala".  System administrators can use
"rscala::scalaInstall(global=TRUE)", which places Scala in the package's
directory but requires a new installation every time the package is updated.
To avoid this, a conventional Scala installation can be performed as described
here: http://www.scala-lang.org/download/install.html.

Error in get(f, envir = ns_env) : 
  Please run "rscala::scalaInstall()" or install Scala manually.
Calls: <Anonymous> -> Filter -> unlist -> lapply -> FUN -> get
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:quantmod':

    summary

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

    summary

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SharpeRatio.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.72 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    www   6.4Mb
Error in re-building vignettes:
  ...

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in c(t(v1) %*% v2y, t(v1) %*% v2x)/(2 * (t(y) %*% v2x)) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'shotGroups.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.80 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘edgeR’
Errors in running code in vignettes:
when running code in ‘SIBER.Rnw’
  ...

> SIBER(y = log(Dat[1, ] + 1), model = "NL")
      mu1       mu2    sigma1    sigma2       pi1     delta        BI 
6.2297063 6.8917722 0.3672838 0.3672838 0.1016360 1.8026005 0.5446901 

> library(edgeR)

  When sourcing ‘SIBER.R’:
Error: there is no package called ‘edgeR’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'SIBER.Rnw' failed with diagnostics:
 chunk 8 
Error in library(edgeR) : there is no package called ‘edgeR’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

The following objects are masked from 'package:base':

    format.pval, round.POSIXt, trunc.POSIXt, units

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

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Loading required package: FME
Loading required package: rootSolve
Loading required package: coda
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'b-simecol-howtos.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.58 \RequirePackage
                    [T1]{fontenc}^^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 'SimInf.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.5 \usepackage
               {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Packages suggested but not available for checking: ‘Rmpi’ ‘copula’
Running ‘doExtras.R’ [1s/1s]
  Comparing ‘doExtras.Rout’ to ‘doExtras.Rout.save’ ... OK
  Running ‘getArray-swap.R’ [1s/2s]
  Running ‘tst-wrongs.R’ [16s/53s]
  Running ‘tstTGforecasts.R’ [5s/18s]
  Running ‘tstVaRsuperadd.R’ [1s/1s]
Running the tests in ‘tests/tstVaRsuperadd.R’ failed.
Last 13 lines of output:
  > ## manually
  > require(copula) # for the following call of doOne()
  Loading required package: copula
  
  > nonGr <- get.nonGrids(varList)$nonGrids
  
  > dd <- doOne(n= min(nonGr$n, 100), d=4, family="Clayton", tau=0.5,
  +             qmargin=nonGr$qmargin, alpha=nonGr$alpha)
  Error in onacopulaL("Clayton", list(th = iTau(archmCopula("clayton"),  : 
    could not find function "onacopulaL"
  Calls: demo -> source -> withVisible -> eval -> eval -> doOne
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'copula'
  Execution halted
Package unavailable to check Rd xrefs: ‘copula’
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

    D, IQR, binom.test, cor, cov, fivenum, median, prop.test,
    quantile, sd, t.test, var

The following objects are masked from 'package:base':

    max, mean, min, prod, range, sample, sum

Loading required package: Sleuth3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chapter01-HortonMosaic.tex' failed.
LaTeX errors:
! LaTeX Error: File `xstring.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hitandrun’
Package unavailable to check Rd xrefs: ‘hitandrun’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 \usepackage
                {diagbox}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.1Mb
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 'pairwiseSNHT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘meteoForecast’
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) :
  swe:Quantity given without unit of measurement: Salinity

Attaching package: ‘xtable’

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

    label

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sos4R.tex' failed.
LaTeX errors:
! LaTeX Error: File `csquotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.19 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’ ‘ALL’
  ‘org.Hs.eg.db’
Packages unavailable to check Rd xrefs: ‘ALL’, ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

The following objects are masked from 'package:base':

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 1.19 secs
Identifing all possible orderings..
Total run time: 1.22 secs
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]="./webshot6a7810b92a16.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6a7810b92a16.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 31.6Mb
  sub-directories of 1Mb or more:
    libs  30.4Mb
span: no visible global function definition for ‘complete.cases’
spanr: no visible global function definition for ‘model.frame’
spanr: no visible global function definition for ‘complete.cases’
spanr.hull: no visible global function definition for ‘par’
spanr.hull: no visible global function definition for ‘plot.new’
spanr.hull: no visible global function definition for ‘plot.window’
spanr.hull: no visible global function definition for ‘axis’
spanr.hull: no visible global function definition for ‘title’
spanr.hull: no visible global function definition for ‘points’
spanr.hull: no visible global function definition for ‘lines’
spanr.hull: no visible global function definition for ‘abline’
spanr.hull: no visible global function definition for ‘text’
spanr.hull: no visible global function definition for ‘segments’
spanr.hull: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/spant.Rcheck/00install.out’ for details.
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.
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]="./webshotdcab656233c5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdcab656233c5.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Smooth interpolated at 279 time(s).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ST_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [unicode,linktocpage=true,bookmarksnumbered=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.6Mb
Package required but not available: ‘MassSpecWavelet’

Package suggested but not available for checking: ‘speaq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘xcms’ ‘MAIT’ ‘genefilter’ ‘impute’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  23.5Mb
lambda.global: no visible global function definition for ‘mad’
lambda.global: no visible global function definition for ‘quantile’
lambda.global: no visible global function definition for ‘qnorm’
lambda.global: no visible global function definition for ‘pnorm’
ls.comp: no visible global function definition for ‘lsfit’
modterritory: no visible global function definition for ‘median’
newgotterritory: no visible global function definition for ‘median’
newterritory: no visible global function definition for ‘median’
ridge.comp: no visible global function definition for ‘lsfit’
ridge.diacomp: no visible global function definition for ‘ls.diag’
sw.plot: no visible global function definition for ‘par’
sw.plot: no visible global function definition for ‘plot’
sw.plot: no visible global function definition for ‘points’
sw.plot: no visible global function definition for ‘image’
sw.plot: no visible global function definition for ‘axis’
sw.plot: no visible global function definition for ‘legend’
sw.plot: no visible global function definition for ‘box’
sw.plot: no visible global function definition for ‘title’
thresh.level: no visible global function definition for ‘na.omit’
thresh.level: no visible global function definition for ‘mad’
thresh.level: no visible global function definition for ‘qnorm’
thresh.level: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis box image legend ls.diag lsfit mad median na.omit par plot pnorm
  points qnorm quantile title
Consider adding
  importFrom("graphics", "axis", "box", "image", "legend", "par", "plot",
             "points", "title")
  importFrom("stats", "ls.diag", "lsfit", "mad", "median", "na.omit",
             "pnorm", "qnorm", "quantile")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Warning in bsplines(mf[[i]], knots = args$knots[[i]]$knots, boundary.knots = args$knots[[i]]$boundary.knots,  :
  Some 'x' values are beyond 'boundary.knots'; Linear extrapolation used.
Warning in (function (xnew)  :
  predictions outside fitted range for lin(glucose).
Warning in (function (xnew)  :
  predictions outside fitted range for sm(glucose).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {algorithm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   5.7Mb
Error in re-building vignettes:
  ...
Loading required package: spray

Attaching package: ‘spray’

The following objects are masked from ‘package:base’:

    pmax, pmin

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Biostrings’ ‘ShortRead’ ‘golubEsets’ ‘RankProd’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sprint.Rcheck/00install.out’ for details.
.dpssToEigenvalues: no visible global function definition for ‘mvfft’
smooth.construct.sp.smooth.spec: no visible global function definition
  for ‘str’
Undefined global functions or variables:
  mvfft str
Consider adding
  importFrom("stats", "mvfft")
  importFrom("utils", "str")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp

Version 3.3 of the spsurvey package was loaded successfully.

Warning in grts(design = Paneldsgn, DesignID = "UNEQUAL", type.frame = "area",  :
  
Oversample size is not proportional to category sample sizes for stratum
"None".

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

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

! Emergency stop.
<read *> 
         
l.7 \bibliographystyle
                      {chicago}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.3Mb
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
draw.srd: no visible global function definition for ‘complete.cases’
draw.srd: no visible global function definition for ‘runif’
draw.srd: no visible global function definition for ‘arrows’
draw.srd: no visible global function definition for ‘text’
draw.srd: no visible global function definition for ‘segments’
draw.srd.enc: no visible global function definition for ‘par’
draw.srd.enc: no visible global function definition for ‘plot.new’
draw.srd.enc: no visible global function definition for ‘plot.window’
draw.srd.enc: no visible global function definition for ‘rgb’
draw.srd.enc: no visible global function definition for ‘polygon’
draw.srd.enc: no visible global function definition for ‘pchisq’
draw.srd.enc: no visible global function definition for ‘text’
draw.srd.enc: no visible global function definition for ‘title’
draw.srd.enc: no visible global function definition for ‘arrows’
drawcell: no visible global function definition for ‘polygon’
drawcell: no visible global function definition for ‘segments’
rotate.srd: no visible global function definition for ‘devAskNewPage’
srd: no visible global function definition for ‘devAskNewPage’
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: spdep
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ssfavignette.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.10 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SSsimple.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.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘easyNCDF’ ‘s2dverification’
Unavailable namespace imported from by a ':::' call: ‘s2dverification’
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: ‘s2dverification’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rpart’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘igraph::dfs’ by ‘RBGL::dfs’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::transitivity’ by ‘RBGL::transitivity’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::bfs’ by ‘RBGL::bfs’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘SteinerNet’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SteinerNet.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
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
Successfully loaded stepR package version 2.0-1.
Several new functions are added in version 2.0-0. Some older functions are deprecated (still working) and may be defunct in a later version. Please read the documentation for more details.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StepR.tex' failed.
LaTeX errors:
! LaTeX Error: File `floatrow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
bos.cat2: no visible global function definition for ‘resid’
bos.cat2: no visible global function definition for ‘lm’
plot.rt: no visible global function definition for ‘plot’
plot.rt: no visible global function definition for ‘text’
plot.rt: no visible global function definition for ‘rect’
plot.rt: no visible global function definition for ‘title’
plot.rt: no visible global function definition for ‘par’
stdata: no visible binding for global variable ‘var’
stima: no visible global function definition for ‘fitted’
stima: no visible global function definition for ‘lm’
stima: no visible global function definition for ‘anova’
stima: no visible global function definition for ‘predict’
stima: no visible global function definition for ‘cor’
stima: no visible global function definition for ‘as.formula’
stima: no visible global function definition for ‘step’
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/tools/bm.sty)

! LaTeX Error: File `tablefootnote.sty' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.22 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on article.log.
make: *** [article.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/stochvol.Rcheck/vign_test/stochvol") : 
  running 'make' failed
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘tigris’
Error in re-building vignettes:
  ...

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Warning: Removed 703 rows containing missing values (geom_point).
Warning: Removed 89 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_path).
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 98-100 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'tigris'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
Running 'texi2dvi' on 'VignetteforSTPGA.ltx' 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.14 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.9Mb
Running ‘test-all.R’ [167s/242s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 00:44:25 2017 
  *********************************************** 
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Packages required but not available: ‘GO.db’ ‘biomaRt’ ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘mutoss’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

The following objects are masked from ‘package:base’:

    as.Date, as.Date.numeric

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'strucchange-intro.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.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘KFKSDS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘genefilter’ ‘sva’
Namespaces in Imports field not imported from:
  ‘doParallel’ ‘matrixStats’ ‘nloptr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/surrosurv.Rcheck/vign_test/surrosurv") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'copulas.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.3 \usepackage
               {amsmath, natbib, hyperref, doi}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘graphite’ ‘curatedOvarianData’ ‘BiocStyle’ ‘org.Hs.eg.db’
Running ‘runTests.R’ [11s/11s]
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_cliqueSurvivalTest.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_cliqueSurvivalTest.R 
  
     test_computePCs.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_computePCs.R 
  
     test_pathwaySurvivalTest.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_pathwaySurvivalTest.R 
  
  
  Error in BiocGenerics:::testPackage("survClip") : 
    unit tests failed for package survClip
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.3Mb
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs  66.1Mb
Package unavailable to check Rd xrefs: ‘survJamda’
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 'plots.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
lines.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘plot’
plot.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘qnorm’
print.survfitr : pfun: no visible global function definition for
  ‘median’
survdiffr: no visible global function definition for ‘runif’
survdiffr: no visible global function definition for ‘terms’
survdiffr: no visible global function definition for ‘model.extract’
survfitr: no visible global function definition for ‘terms’
survfitr: no visible global function definition for ‘model.extract’
Undefined global functions or variables:
  lines median model.extract plot qnorm runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median", "model.extract", "qnorm", "runif",
             "terms")
to your NAMESPACE file.
File ‘survrec/libs/survrec.so’:
  Found ‘__gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.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.
Error in re-building vignettes:
  ...
Loading required package: SurvRegCensCov
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'weibull.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.3 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svUnit.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
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SWATmodel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sybilSBML.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mpoly’
Running examples in ‘symmoments-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Errors in running code in vignettes:
when running code in ‘symmoments.rnw’
  ...
[4,]    1    1    1    2

> evaluate(m1234, c(4, 2, 1, 1, 3, 1, 1, 2, 1, 2))
[1] 3480

> library(mpoly)

  When sourcing ‘symmoments.R’:
Error: there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

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

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    single


Error: processing vignette 'symmoments.rnw' failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Packages suggested but not available for checking: ‘tigris’ ‘rgdal’
Packages suggested but not available for checking: ‘GISTools’ ‘rgeos’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘tcpl_Overview.Rnw’
  ...
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

  When sourcing ‘tcpl_Overview.R’:
Error: argument to 'which' is not logical
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tdthap-paper.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.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘boot’ ‘survrec’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: textutils

Attaching package: 'textutils'

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

    toHTML

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

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Tides
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(wet$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(wet$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tides.tex' failed.
BibTeX errors:
The top-level auxiliary file: Tides.aux
I couldn't open style file apalike2.bst
---line 14 of file Tides.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file Tides.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘ggtree’ ‘treeio’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
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: ggplot2

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 111-113 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for ‘var’
sampleObs,tDist-numeric: no visible global function definition for ‘rt’
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in ‘tileHMM.Rnw’
  ...

> h3k27.data <- as.matrix(simChIP[, 7:14])

> h3k27.data <- log(h3k27.data, 2)

> h3k27.norm <- preprocessCore::normalize.quantiles(h3k27.data)

  When sourcing ‘tileHMM.R’:
Error: there is no package called ‘preprocessCore’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'tileHMM.Rnw' failed with diagnostics:
 chunk 3 
Error in loadNamespace(name) : 
  there is no package called ‘preprocessCore’
Execution halted
'library' or 'require' call to ‘ggplot2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘microbenchmark’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  ‘microbenchmark’
do_timeit: no visible global function definition for ‘Rprof’
do_timeit: no visible global function definition for ‘summaryRprof’
mean.timeit: no visible global function definition for ‘aggregate’
plot.timeit: no visible global function definition for ‘ggplot’
plot.timeit: no visible global function definition for ‘aes’
plot.timeit: no visible global function definition for ‘geom_boxplot’
plot.timeit: no visible global function definition for ‘geom_point’
plot.timeit: no visible global function definition for ‘xlab’
plot.timeit: no visible global function definition for ‘ylab’
plot.timeit: no visible global function definition for ‘ggtitle’
plot.timeit: no visible global function definition for ‘coord_flip’
timeit: no visible binding for global variable ‘median’
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
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 'tmle-npvi.tex' failed.
LaTeX errors:
! LaTeX Error: File `manfnt.sty' not found.

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

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [textwidth=15cm, textheight=23cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Expanding_TR8.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {graphicx}^^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 'traitr.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.15 \usepackage
                {amsmath}            % for amslatex stuff^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘OpenStreetMap’
Package unavailable to check Rd xrefs: ‘rgeos’
Running ‘tracks.R’ [2s/3s]
Running the tests in ‘tests/tracks.R’ failed.
Complete output:
  > Sys.setenv(TZ = "Europe/Berlin")
  > # Load required libraries.
  > 
  > library(sp)
  > library(spacetime)
  > library(trajectories)
  > library(rgdal)
  Error in library(rgdal) : there is no package called 'rgdal'
  Execution halted
Error in re-building vignettes:
  ...
Warning in add.known.TRAMPknowns(x$knowns, x$samples, sample.fk, ...) :
  Mutiple peaks per enzyme/primer combination for sample 221, taking largest peaks only
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TRAMPRdemo.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.3 \usepackage
               {Sweave}^^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 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'trapezoid.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘treeHFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawViterbiTree
> ### Title: Arranges a Viterbi tree
> ### Aliases: DrawViterbiTree
> ### Keywords: misc
> 
> ### ** Examples
> 
> ## Fit a continous treeHFM ## 
> nHStates = 2;
> ########create observation sequences########
> obs1 <- rbind(runif(10,0,1),runif(10,0,1))
> obs2 <- rbind(runif(8,0,1),runif(8,0,1))
> data=list()
> data[[1]]=obs1
> data[[2]]=obs2
> ######### create guesses for gaussian covariance matrix and means #########
> mc2 <- Mclust(t(cbind(obs1,obs2)), G=2)
> muInit=mc2$parameters$mean;
> SigmaInit=mc2$parameters$variance$sigma
> #########create tree topology####################################
> nodeIndices1=cbind(c(0,1,2,3,3,4,5,6,7,8),c(1,2,3,4,5,6,7,8,9,10));
> nodeIndices2=cbind(c(0,1,2,3,4,4,5,6),c(1,2,3,4,5,6,7,8));
> dataNodeIndices=list()
> dataNodeIndices[[1]]=nodeIndices1;
> dataNodeIndices[[2]]=nodeIndices2;
> ######### create guesses for prior and transition matrices#########
> prior1=array(1,nHStates);
> priorInit = array(1,nHStates)/nHStates;
> transmatInit = matrix(1,nHStates,nHStates)*(1/nHStates);
> transInitDiv= matrix(1,nHStates,nHStates*nHStates)*(1/(nHStates*nHStates))
> #
> hfm=HFMfit(data,nHStates,dataNodeIndices,priorInit,transmatInit,transInitDiv,'c',
+ SigmaInit=SigmaInit, muInit=muInit);

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: .Call("RWrapperBM", priorInit, transmatInit, transInitDiv, emissionProb,     data, nodeIndices, parents, summationIndices, indicesXD,     type, stateIndicesSingle, nHStates, nDStates, nObs, dimData,     nEStates, SigmaInit, muInit)
 2: HFMfit(data, nHStates, dataNodeIndices, priorInit, transmatInit,     transInitDiv, "c", SigmaInit = SigmaInit, muInit = muInit)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
negative edges length changed to 0!
Quitting from lines 115-133 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/tsBSS.Rcheck/00install.out’ for details.
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 'Umpire.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \pagestyle
               {myheadings}^^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 '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
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.
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
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MedRegExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
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:
  ...

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.
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.
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
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.
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
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/soccer2-plot1-1-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 `figure/goggles-plot1-1-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 `figure/swim-plot1-1-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 `figure/swim2-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Package suggested but not available for checking: ‘GenomicScores’
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.
Found the following significant warnings:
  Warning: D:/temp/RtmpI17xRi/R.INSTALL391c56a8240e/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/ACEt.Rcheck/00install.out' for details.
prepare_Rd: ACEt-package.Rd:1: All text must be in a section
Authors@R field gives persons with no valid roles:
  Anders Hedenström [fnd]
Package suggested but not available for checking: 'gge'
Running examples in 'agridat-Ex.R' failed
The error most likely occurred in:

> ### Name: crossa.wheat
> ### Title: Multi-environment trial of wheat for 18 genotypes at 25
> ###   locations
> ### Aliases: crossa.wheat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(crossa.wheat)
> dat <- crossa.wheat
> 
> # AMMI biplot.  Fig 3 of Crossa et al.
> if(require(agricolae)){
+   m1 <- with(dat, AMMI(E=loc, G=gen, R=1, Y=yield))
+   b1 <- m1$biplot[,1:4]
+   b1$PC1 <- -1 * b1$PC1 # Flip vertical
+   plot(b1$yield, b1$PC1, cex=0.0,
+        text(b1$yield, b1$PC1, cex=.5, labels=row.names(b1),col="brown"),
+        main="crossa.wheat AMMI biplot", xlab="Average yield", ylab="PC1", frame=TRUE)
+   mn <- mean(b1$yield)
+   abline(h=0, v=mn, col='wheat')
+ 
+   g1 <- subset(b1,type=="GEN")
+   text(g1$yield, g1$PC1, rownames(g1), col="darkgreen", cex=.5)
+ 
+   e1 <- subset(b1,type=="ENV")
+   arrows(mn, 0,
+          0.95*(e1$yield - mn) + mn, 0.95*e1$PC1,
+          col= "brown", lwd=1.8,length=0.1)
+ }
Loading required package: agricolae
> 
> # GGB example
> library(agridat)
> data(crossa.wheat)
> dat2 <- crossa.wheat
> 
> # FIXME: The loc grouping is now in the data
> 
> # Define mega-environment groups of locations
> dat2$eg <- ifelse(is.element(dat2$loc,
+                              c("KN","NB","PA","BJ","IL","TC",
+                                "JM","PI","AS","ID","SC","SS",
+                                "SJ","MS","MG","MM")), "Grp1", "Grp2")
> 
> library(gge)
Error in library(gge) : there is no package called 'gge'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 44-53 (agridat_examples.Rmd) 
Error: processing vignette 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'gge'
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 1. Failure: Downloaded data is as expected (@test_download.R#29)  -----------
  get_fred_series(...) not equal to data.frame(date = as.Date("2009-03-01"), test = 89.1913).
  Component "test": Mean relative difference: 0.002053736
  
  -- 2. Failure: Downloaded data is as expected (@test_download.R#36)  -----------
  dplyr::filter(get_fred_series("INDPRO", "test"), date == "2009-03-01") not equal to data.frame(date = as.Date("2009-03-01"), test = 89.1913).
  Component "test": Mean relative difference: 0.002053736
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Downloaded data is as expected (@test_download.R#29) 
  2. Failure: Downloaded data is as expected (@test_download.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/apTreeshape.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'trtf'
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/audio.Rcheck/00install.out' for details.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.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.
Found the following significant warnings:
  Warning: replacing previous import 'spam::det' by 'Matrix::det' when loading 'bamlss'
See 'd:/Rcompile/CRANpkg/local/3.3/bamlss.Rcheck/00install.out' for details.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/bayesCL.Rcheck/00install.out' for details.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.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.
Authors@R field gives persons with no valid roles:
  Bea Hernández [rev] (Bea reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
  Elaine McVey [rev] (Elaine reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
Running 'testthat.R' [74s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: store_bikedata(data_dir = tempdir(), bikedb = bikedb, quiet = TRUE)
  10: rcpp_import_stn_df(bikedb, lo_stns, "lo")
  
  == testthat results  ===========================================================
  OK: 139 SKIPPED: 1 FAILED: 1
  1. Error: write and store data (@test-store-data.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'csaw'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-04-02 21:59:06] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  == testthat results  ===========================================================
  OK: 59 SKIPPED: 0 FAILED: 5
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: initial (@test_install_uilts.R#39) 
  4. Error: dependence (@test_install_uilts.R#88) 
  5. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  `Time Period` = col_character()
)
See spec(...) for full column specifications.

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union


Attaching package: 'zoo'

The following objects are masked from 'package:base':

    as.Date, as.Date.numeric

Quitting from lines 61-79 (BIS.Rmd) 
Error: processing vignette 'BIS.Rmd' failed with diagnostics:
Faceting variables must have at least one value
Execution halted
Running examples in 'bmrm-Ex.R' failed
The error most likely occurred in:

> ### Name: mmc
> ### Title: Convenient wrapper function to solve max-margin clustering
> ###   problem on a dataset
> ### Aliases: mmc
> 
> ### ** Examples
> 
>    # -- Prepare a 2D dataset to cluster with an intercept
>    x <- cbind(intercept=100,scale(data.matrix(iris[c(1,3)]),center=TRUE,scale=FALSE))
> 
>    # -- Find max-margin clusters
>    y <- mmc(x,k=3,LAMBDA=0.001,minClusterSize=10,seeds=5)
Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column
Calls: mmc ... merge.default -> merge -> merge.data.frame -> fix.by
Execution halted
Package suggested but not available for checking: 'ASGS.foyer'
Authors@R field gives persons with no valid roles:
  Brooke Anderson <brooke.anderson@colostate.edu> [rev] (0000-0002-5012-9035)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BPEC.Rcheck/00install.out' for details.
Running examples in 'BrailleR-Ex.R' failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Running examples in 'broom-Ex.R' failed
The error most likely occurred in:

> ### Name: kde_tidiers
> ### Title: Tidy a kernel density estimate object from the ks package
> ### Aliases: kde_tidiers tidy.kde
> 
> ### ** Examples
> 
> 
> if (require("ks", quietly = TRUE)) {
+   dat <- replicate(2, rnorm(100))
+   k <- kde(dat)
+   
+   td <- tidy(k)
+   head(td)
+   
+   library(ggplot2)
+   ggplot(td, aes(x1, x2, fill = estimate)) +
+     geom_tile() +
+     theme_void()
+   
+   # also works with 3 dimensions
+   dat3 <- replicate(3, rnorm(100))
+   k3 <- kde(dat3)
+   
+   td3 <- tidy(k3)
+   head(td3)
+ }
Note: method with signature 'Matrix#diagonalMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#ddiMatrix'.
 "sparseMatrix#ANY" would also be valid
Note: method with signature 'dsparseMatrix#dsparseMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#dtTMatrix'.
 "sparseMatrix#TsparseMatrix" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: kde -> Hpi -> gdscalar -> norm -> norm
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File 'camel/libs/i386/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'
File 'camel/libs/x64/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.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.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "causaleffect.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
running 'texi2dvi' on 'causaleffect.ltx' failed

LaTeX errors:
tes/causaleffect.ltx:81: LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help
You're in trouble here.  Try typing  <return>  to proceed.
Execution halted
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Running 'test-all.R' [26s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
regularize.values: possible error in xy.coords(x, y, setLab = FALSE):
  unused argument (setLab = FALSE)
Running 'SP500-ex.R' [35s]
Running the tests in 'tests/SP500-ex.R' failed.
Last 13 lines of output:
  +     dim(spWts.non0 <- spWts[rowSums(spWts) > 0 , ])
  +     round(1000 * spWts.non0)
  +     ##
  +     image(spWts.non0, xlab = "turning point", ylab = "asset number")
  +     wts.non0 <- as(spWts.non0, "matrix")
  + }) else {
  +     warning("'Matrix' package not available -- should not happen!")
  +     wts.non0 <- CLs5c.0.120$weights_set[rowSums(CLs5c.0.120$weights_set) > 0 , ]
  +     if(is.null(colnames(wts.non0))) ## empty column names for nice printing:
  +         colnames(wts.non0) <- rep("", ncol(wts.non0))
  +     print.table(round(1000 * wts.non0), zero.print=".")
  + }
  Loading required package: Matrix
  Error: could not find function "withAutoprint"
  Execution halted
Package suggested but not available for checking: 'SingleCellExperiment'
Unknown package 'SingleCellExperiment' in Rd xrefs
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SingleCellExperiment'
Error in .requirePackage(package) : 
  unable to find required package 'SingleCellExperiment'
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 143-147 (clustree.Rmd) 
Error: processing vignette 'clustree.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
Execution halted
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: 'XML'

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'moe430a.db'
Loading required package: RankAggreg
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "clValid.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'clValid.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE (file ./clValid-022.pdf): PDF inclusion: required p
age does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Execution halted
Authors@R field gives persons with no valid roles:
  Anna Krystalli [rev] (0000-0002-2378-4915)
  Toph Allen [rev] (0000-0003-4580-091X)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/cometExactTest.Rcheck/00install.out' for details.
Packages required and available but unsuitable versions: 'graphics' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Running 'testthat.R' [100s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [125s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Cyclops.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  R Consortium [fnd]
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         "stack"), class = "Rcpp_stack_trace")), .Names = c("message", "call", "cppstack"
     ), class = c("Rcpp::exception", "C++Error", "error", "condition")))
  
  Error in stop(list(message = "Failed to connect: Can't connect to MySQL server on 'localhost' (0)",  : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... <Anonymous> -> .local -> connection_create -> .Call
  == testthat results  ===========================================================
  OK: 536 SKIPPED: 11 FAILED: 4
  1. Error: explicit collection returns all data (@test-collect.R#13) 
  2. Error: (unknown) (@test-collect.R#11) 
  3. Error: explicit collection returns all data (@test-collect.R#13) 
  4. Error: (unknown) (@test-collect.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 4. Failure: DCF reader works (@test-read.R#9)  ------------------------------
  desc$get("Author") not equal to c(Author = "Gábor Csárdi").
  1/1 mismatches
  x[1]: "GÃ¡bor CsÃ¡rdi"
  y[1]: "Gábor Csárdi"
  
  == testthat results  ===========================================================
  OK: 348 SKIPPED: 0 FAILED: 4
  1. Failure: get_maintainer is OK, too (@test-authors.R#171) 
  2. Failure: get works (@test-queries.R#9) 
  3. Failure: get_or_fail works (@test-queries.R#18) 
  4. Failure: DCF reader works (@test-read.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'has-devel.R' [2s]
  Running 'test-that.R' [99s]
Running the tests in 'tests/test-that.R' failed.
Last 13 lines of output:
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 399 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'AESTest.R' [0s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [1s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [0s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
Running 'AESTest.R' [0s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [0s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [0s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
package 'diversitree' exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/diversitree.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: expect_identical(summarise(gdf, out = !(!1:2)), tibble(g = c(1, 2), out = 1:2)) at testthat/test-summarise.r:985
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  == testthat results  ===========================================================
  OK: 2876 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1: expect_identical(summarise(gdf, out = !(!1:2)), tibble(g = c(1, 2), out = 1:2)) at testthat/test-summarise.r:985
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: summarise(gdf, out = 1:2)
  5: summarise.tbl_df(gdf, out = 1:2)
  6: summarise_impl(.data, dots)
  
  == testthat results  ===========================================================
  OK: 2876 SKIPPED: 6 FAILED: 3
  1. Error: mutate() supports unquoted values (@test-mutate.r#721) 
  2. Failure: summarise() supports unquoted values (@test-summarise.r#980) 
  3. Error: summarise() supports unquoted values (@test-summarise.r#985) 
  
  Error: testthat unit tests failed
  Execution halted
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.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.
Authors@R field gives persons with no valid roles:
  Ben Marwick <bmarwick@uw.edu> [rev]
  Peter Slaughter <slaughter@nceas.ucsb.edu> [rev]
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
File 'EBS/libs/i386/EBS.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'GeneralFunctions.o'
File 'EBS/libs/x64/EBS.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'GeneralFunctions.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.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("ECctmc")
  -- 1. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  -- 2. Failure: Modified rejection sampling and uniformization target the same di
  t.test(MR_res[k, ], Unif_res[k, ])$p.value < 0.1 isn't false.
  
  == testthat results  ===========================================================
  OK: 5 SKIPPED: 0 FAILED: 2
  1. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  2. Failure: Modified rejection sampling and uniformization target the same distribution (@test_simfcns.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

The following objects are masked from 'package:stats':

    filter, lag

The following objects are masked from 'package:base':

    intersect, setdiff, setequal, union

Quitting from lines 108-113 (parsing.Rmd) 
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'scales'

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

    discard


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'GGally'

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

    nasa

Quitting from lines 337-354 (exploring-election-data.Rmd) 
Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics:
could not find function "dmap"
Execution halted
File 'elrm/libs/i386/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'
File 'elrm/libs/x64/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/emdi.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
ggtree v1.6.11  For help: https://guangchuangyu.github.io/ggtree

If you use ggtree in published research, please cite:
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Missing or unexported object: 'xcms::profMat'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/EValue.Rcheck/00install.out' for details.
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Universidade Federal de Santa Maria <ppgcs@ufsm.br> [fnd]
Package required but not available: 'CVXR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Warning: invalid input found on input connection 'fivethirtyeight-Ex.R'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/flowDiv.Rcheck/00install.out' for details.
Running examples in 'foghorn-Ex.R' failed
The error most likely occurred in:

> ### Name: cran_results
> ### Title: Table of the CRAN check results
> ### Aliases: cran_results
> 
> ### ** Examples
> 
>   if (curl::has_internet()) {
+     cran_results(pkg="MASS")
+   }
Error: Invalid package name(s): 'MASS'.
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("foghorn")
  -- 1. Error: check output for MASS (@test-foghorn.R#332)  ----------------------
  Invalid package name(s): 'MASS'.
  1: cran_results(pkg = "MASS") at testthat/test-foghorn.R:332
  2: cran_results_web(email, pkg, ...)
  3: read_cran_web_from_pkg(pkg, ...)
  4: stop("Invalid package name(s): ", paste(sQuote(pkg[bad]), collapse = ", "), ".", 
         call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 11 SKIPPED: 17 FAILED: 1
  1. Error: check output for MASS (@test-foghorn.R#332) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 23-25 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
Invalid email address(es): 'francois.michonneau@gmail.com'.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FRESA.CAD.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.5Mb
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3, 3).
  Lengths differ: 5 is not 6
  
  -- 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 2, 3).
  Lengths differ: 5 is not 6
  
  == testthat results  ===========================================================
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#56) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'GAMens-Ex.R' failed
The error most likely occurred in:

> ### Name: GAMens
> ### Title: Applies the GAMbag, GAMrsm or GAMens ensemble classifier to a
> ###   data set
> ### Aliases: GAMens
> ### Keywords: models classif
> 
> ### ** Examples
> 
> 
> ## Load data (mlbench library should be loaded)
> library(mlbench)
> data(Ionosphere)
> 
> ## Train a GAMens ensemble,
> ## estimated using 4 nonparametric terms and 2 linear terms
> Ionosphere.GAMens <- GAMens(Class~s(V3,4)+s(V4,4)+s(V5,3)+s(V6,5)+V7+V8,
+ Ionosphere ,3 , autoform=FALSE, iter=10 )
Error: could not find function "predict.gam"
Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
Package required but not available: 'gge'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'nipals'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required and available but unsuitable version: 'grid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'base2grob'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ggstatsplot.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Error in re-building vignettes:
  ...
trying URL 'http://web.stanford.edu/~hastie/glmnet/glmnetData/Leukemia.RData'
Content type '' length 2030255 bytes (1.9 MB)
==================================================
downloaded 1.9 MB

Quitting from lines 176-182 (intro.rmd) 
Error: processing vignette 'intro.rmd' failed with diagnostics:
'x' and 'w' must have the same length
Execution halted
Authors@R field gives persons with no valid roles:
  Neal Richardson <neal.p.richardson@gmail.com> [rev] (Neal reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
  Julia Gustavsen <j.gustavsen@gmail.com> [rev] (Julia reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Invalid citation information in 'inst/CITATION':
  Error in .citation(rval): attempt to set an attribute on NULL
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:

======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Package required but not available: 'hexSticker'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
3/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Package required and available but unsuitable version: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'ggimage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Error in library.dynam(lib, package, package.lib) : 
  DLL 'diversitree' not found: maybe not installed for this architecture?
Quitting from lines 24-37 (hisse-vignette.Rmd) 
Error: processing vignette 'hisse-vignette.Rmd' failed with diagnostics:
package or namespace load failed for 'diversitree'
Execution halted
Package suggested but not available for checking: 'trackr'
Package required and available but unsuitable version: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  The R Consortium [fnd]
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.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.
Running 'testthat.R' [112s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 83 SKIPPED: 17 FAILED: 11
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9) 
  3. Error: phyloseq sim (@test-HTSSIP_sim.R#59) 
  4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75) 
  5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 
  6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  8. Error: phyloseq_re sample_data can be converted to dataframe (@test-Util.R#35) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Dscores: no visible global function definition for 'filter'
Dscores: no visible global function definition for 'sd'
Gscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'object.size'
RobustScores: no visible global function definition for 'filter'
SplitHalf: no visible global function definition for 'cor'
TestRetest: no visible global function definition for 'filter'
TestRetest: no visible global function definition for 'cor'
WPRscores: no visible global function definition for 'filter'
WPRscores: no visible global function definition for 'quantile'
WPRscores: no visible global function definition for 'sd'
computeMinid: no visible global function definition for 'sd'
doP1P2: no visible global function definition for 'filter'
doP1P2: no visible global function definition for 'sd'
doP1P2P3P4: no visible global function definition for 'filter'
specialvar: no visible global function definition for 'var'
Undefined global functions or variables:
  cor filter object.size quantile sd var
Consider adding
  importFrom("stats", "cor", "filter", "quantile", "sd", "var")
  importFrom("utils", "object.size")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    3.2Mb
    libs   2.9Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         val
     })(Assessment.StockCode = "cod.27.47d20", Assessment.AssessmentYear = 2015L, Assessment.ContactPerson = "colin.millar@ices.dk", 
         Assessment.NameSystemProducedFile = "icesSAG R package version 1.3.2", Assessment.Fish_Data.Year = 2000L, 
         Assessment.Fish_Data.Year = 2001L, Assessment.Fish_Data.Year = 2002L, Assessment.Fish_Data.Year = 2003L, 
         Assessment.Fish_Data.Year = 2004L, Assessment.Fish_Data.Year = 2005L, Assessment.Fish_Data.Year = 2006L, 
         Assessment.Fish_Data.Year = 2007L, Assessment.Fish_Data.Year = 2008L, Assessment.Fish_Data.Year = 2009L, 
         Assessment.Fish_Data.Year = 2010L, Assessment.Fish_Data.Year = 2011L, Assessment.Fish_Data.Year = 2012L, 
         Assessment.Fish_Data.Year = 2013L, Assessment.Fish_Data.Year = 2014L, Assessment.Fish_Data.Year = 2015L)
  
  == testthat results  ===========================================================
  OK: 1334 SKIPPED: 0 FAILED: 1
  1. Error: SAG upload (@test-test.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Andee Kaplan [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
  Carl Ganz [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpqwXtIK\ex_data1297019d7404.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpqwXtIK\ex_data1297019d7404.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
Package required and available but unsuitable version: 'libcoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace with empty importFrom: 'miscTools'
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant number: MR/M013227/1)
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant numbers: G0400615 and MR/M013227/1)
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: jpmesh
  This package provide map data is based on the Digital Map 25000(Map
  Image) published by Geospatial Information Authorityof Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  -- 1. Failure: jpn_pref (@test-spdf_jpn.R#20)  ---------------------------------
  Names of `df_pref2` ('jis_code', 'prefecture', 'geometry') don't match 'jis_code', 'prefecture', '.'
  
  == testthat results  ===========================================================
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: jpn_pref (@test-spdf_jpn.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
StartKappa: no visible global function definition for 'read.csv'
StartKappa: no visible global function definition for 'na.omit'
StartKappa: no visible global function definition for 'write.csv2'
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> # Basic usage with default arguments
> result = knockoff.filter(X, y, knockoffs=knockoffs,
+                            statistic=stat.stability_selection)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 89 99
> 
> # Advanced usage with custom arguments
> foo = stat.stability_selection
> k_stat = function(X, X_k, y) foo(X, X_k, y, fitfun=stabs::lars.lasso)
> result = knockoff.filter(X, y, knockoffs=knockoffs, statistic=k_stat)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 65 89 99
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  53.32 1.16 54.77 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running examples in 'ks-Ex.R' failed
The error most likely occurred in:

> ### Name: Hpi
> ### Title: Plug-in bandwidth selector
> ### Aliases: Hpi Hpi.diag hpi
> ### Keywords: smooth
> 
> ### ** Examples
> 
> data(unicef)
> Hpi(unicef, pilot="dscalar")
Note: method with signature 'ANY#sparseMatrix' chosen for function 'kronecker',
 target signature 'dgeMatrix#dtTMatrix'.
 "Matrix#ANY" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: Hpi -> gdscalar -> norm -> norm
Execution halted
Authors@R field gives persons with no valid roles:
  Laura Graham [rev] (Laura reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
  Jeffrey Hollister [rev] (Jeffrey reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/languageserver.Rcheck/00install.out' for details.
File 'leaps/libs/i386/leaps.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'leaps.o'
File 'leaps/libs/x64/leaps.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'leaps.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  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in 'lmem.gwaser-Ex.R' failed
The error most likely occurred in:

> ### Name: mq.g.diagnostics
> ### Title: Performs molecular markers quality diagnostics.
> ### Aliases: mq.g.diagnostics
> 
> ### ** Examples
> 
> data (QA_geno)
> data (QA_map)
> data (QA_pheno)
> 
> P.data <- QA_pheno
> G.data <- QA_geno
> map.data <- QA_map
> 
> cross.data  <- gwas.cross (P.data, G.data, map.data,
+ cross='gwas', heterozygotes=FALSE)
 --Read the following data:
	 179  individuals
	 811  markers
	 3  phenotypes
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
 --Cross type: bc 
> summary (cross.data)
Warning in summary.cross(cross.data) :
  Some markers at the same position on chr 1,2,3,4,5,6,7; use jittermap().
    Doubled haploids

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

    No. chromosomes:    7 
        Autosomes:      1 2 3 4 5 6 7 

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in mq_missinggenotype_plot(crossobj) : 
  could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Package required and available but unsuitable version: 'partykit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 3, minute = 36, second = 5, dt = structure(1522719371.22966, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2429 SKIPPED: 4 FAILED: 6
  1. Error: Comparison operators work with POSIX and Date objects (@test-ops-compare.R#4) 
  2. Error: difftime comparison with periods works (@test-ops-compare.R#63) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  4. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  5. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  6. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 3, minute = 36, second = 5, dt = structure(1522719400.41708, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: (function (...) 
     .subset2(public_bind_env, "finalize")())(<environment>)
  10: .subset2(public_bind_env, "finalize")()
  11: is_open(self$con)
  12: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: The pipe function (@test_nse.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: row_ievora(x = x, g = grp)
  7: row_t_welch(x[, g == 1, drop = FALSE], x[, g == 0, drop = FALSE])
  8: rowSums((x - mxs)^2, na.rm = TRUE)
  9: stop("'x' must be an array of at least two dimensions")
  
  == testthat results  ===========================================================
  OK: 820 SKIPPED: 0 FAILED: 4
  1. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cases.R#48) 
  2. Error: groups can all be NA (@test-parameters-special-cases.R#103) 
  3. Error: groups can all be NaN (@test-parameters-special-cases.R#113) 
  4. Error: all observations can be in the same group (@test-parameters-special-cases.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
File 'maxent/libs/i386/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'
File 'maxent/libs/x64/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.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  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.2     v dplyr   0.7.4
v tidyr   0.8.0     v stringr 1.3.0
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Loading required package: lattice
Error in unloadNamespace(package) : 
  namespace 'lattice' is imported by 'nlme', 'Matrix', 'psych', 'mosaic' so cannot be unloaded
Error : .onAttach failed in attachNamespace() for 'mdsr', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package 'lattice' version 0.20.35 cannot be unloaded
Error: package or namespace load failed for 'mdsr'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Mega2R.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
File 'MigClim/libs/i386/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.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.
Missing or unexported object: 'tools::CRAN_package_db'
Package required and available but unsuitable version: 'S4Vectors'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'run-base.R' [567s]
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  7: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  8: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  9: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  == testthat results  ===========================================================
  OK: 3549 SKIPPED: 0 FAILED: 3
  1. Error: measures (@test_base_measures.R#53) 
  2. Error: check measure calculations (@test_base_measures.R#756) 
  3. Error: predict preserves rownames (@test_base_predict.R#92) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'run-base.R' [10m]
Running the tests in 'tests/run-base.R' failed.
Last 13 lines of output:
  7: addClasses(makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, 
         name, short.name, note, callees), c(cl, "RLearnerClassif"))
  8: makeRLearnerInternal(cl, "classif", package, par.set, par.vals, properties, name, 
         short.name, note, callees)
  9: requirePackages(package, why = stri_paste("learner", id, sep = " "), default.method = "load")
  10: stopf("For %s please install the following packages: %s", why, ps)
  
  == testthat results  ===========================================================
  OK: 3549 SKIPPED: 0 FAILED: 3
  1. Error: measures (@test_base_measures.R#53) 
  2. Error: check measure calculations (@test_base_measures.R#756) 
  3. Error: predict preserves rownames (@test_base_predict.R#92) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/monoreg.Rcheck/00install.out' for details.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test-all.R' [2s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
     2, 2), second = c(24.0832331180573, 24.0832331180573, 24.0832331180573, 24.0832331180573, 
     24.0832331180573, 24.0832331180573), dt = structure(c(1017781344.08323, 1017781344.08323, 
     1017781344.08323, 1049317344.08323, 1049317344.08323, 1080939744.08323), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 3
  1. Error: Cumulative measures (@test-TriangleConstruction.R#5) 
  2. Error: Incremental measures (@test-TriangleConstruction.R#23) 
  3. Error: Multiple stochastic measures (@test-TriangleConstruction.R#41) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.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.
Authors@R field gives persons with no valid roles:
  YouGov [fnd]
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/MSeasy.Rcheck/00install.out' for details.
Running examples in 'NAM-Ex.R' failed
The error most likely occurred in:

> ### Name: GWP
> ### Title: Genome-wide prediction
> ### Aliases: wgr ben
> 
> ### ** Examples
> 
> # Load data
> data(tpod)
> 
> # BLUP
> BRR = wgr(y,gen,iv=FALSE,pi=0,it=200,bi=50)
> cor(y,BRR$hat)
          [,1]
[1,] 0.6981897
> 
> # BayesA
> BayesA = wgr(y,gen,iv=TRUE,pi=0,it=200,bi=50)
> cor(y,BayesA$hat)
          [,1]
[1,] 0.6919416
> 
> # BayesB
> BayesB = wgr(y,gen,iv=TRUE,pi=.95,it=200,bi=50)
> cor(y,BayesB$hat)
          [,1]
[1,] 0.5943869
> 
> # BayesC
> BayesC = wgr(y,gen,iv=FALSE,pi=.95,it=200,bi=50)
> cor(y,BayesC$hat)
          [,1]
[1,] 0.4894693
> 
> # BayesL
> BayesL = wgr(y,gen,de=TRUE,it=200,bi=50)
> cor(y,BayesL$hat)
          [,1]
[1,] 0.6558428
> 
> # Bagging  BLUP
> Bag = wgr(y,gen,bag=0.999,it=200,bi=50)
> cor(y,Bag$hat)
          [,1]
[1,] 0.5964858
> 
> # Subsampling  BLUP
> Sub = wgr(y,gen,bag=0.5,it=200,bi=50)
Error in crossprod(x, y) : 
  requires numeric/complex matrix/vector arguments
Calls: wgr -> crossprod
Execution halted
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 4, minute = 10, second = 42.2364139556885, dt = structure(1522721440.23641, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 3
  1. Error: character date handling: yyyy-mm-dd hh:mm:ss in past (@test-naptime.R#126) 
  2. Error: character date handling: yyyy-mm-dd hh:mm:ss in future (@test-naptime.R#136) 
  3. Error: Invalid Period throws error (@test-naptime.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.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.
File 'NetSim/libs/i386/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'
File 'NetSim/libs/x64/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.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.
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             cat(msg)
         if (length(msg) == 0) {
             e = simpleError(paste(1:length(messages), messages, sep = ": ", collapse = ""))
             class(e) = c(class, class(e))
             stop(e)
         }
         messages <<- c(messages, msg)
     })(character(0))
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-NFP.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.3Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/nlcv.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

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

Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Authors@R field gives persons with no valid roles:
  Julia Silge [rev] (Julia Silge reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/36.)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMPController.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMx.Rcheck/00install.out' for details.
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'CVXR'

Package suggested but not available for checking: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 556 SKIPPED: 0 FAILED: 2
  1. Error: interval: year (@test_thicken_integration.R#7) 
  2. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 572 SKIPPED: 0 FAILED: 1
  1. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/PANDA.Rcheck/00install.out' for details.
Packages required and available but unsuitable versions: 'libcoin' 'inum'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Error: (unknown) (@test_GTE-summary_by.R#7) 
  2. Error: all queries match expected values (@test_GTE_paper_count.R#132) 
  3. Error: document type = *journal-paper* matches (@test_document_type.R#11) 
  4. Error: document type = *conference-paper* matches (@test_document_type.R#22) 
  5. Error: make_search_url matches number of papers from_year to_year (@test_from_year_to_year.R#12) 
  6. Error: is_dctype_enabled = FALSE (@test_is_dctype_enabled.R#8) 
  7. Error: is_dctype_enabled = TRUE (@test_is_dctype_enabled.R#21) 
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 5 (https://www.onepetro.org/search?q=smartwell&peer_reviewed=&published_between=&from_year=&to_year=) 
  Execution halted
Package required and available but unsuitable version: 'qusage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.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.
Error in re-building vignettes:
  ...
URL: http://plotkml.r-forge.r-project.org/
Loading required package: GSIF
GSIF version 0.5-4 (2017-04-25)
URL: http://gsif.r-forge.r-project.org/

Attaching package: 'XML'

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

    toHTML

Reprojecting to +proj=longlat +datum=WGS84 ...
KML file opened for writing...
Writing to KML...
Closing  eberg.ll__CLYMHT_A__.kml
KML file opened for writing...
Writing to KML...
Closing  eberg.ll.kml
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...

Error: processing vignette 'jss1079.Rnw' failed with diagnostics:
 chunk 12 
Error in paths(show.paths = TRUE) : object 'saga.version' not found
Execution halted
pointdensity: no visible global function definition for
  'txtProgressBar'
pointdensity: no visible global function definition for
  'setTxtProgressBar'
pointdensity: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "flush.console", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.eg.db'
  'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db' 'org.Pf.plasmo.db'
  'org.Xl.eg.db'
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ..
  ..
  == testthat results  ===========================================================
  OK: 8417 SKIPPED: 53 FAILED: 8
  1. Error: compile (@test_add_connected_constraints.R#12) 
  2. Error: (unknown) (@test_add_connected_constraints.R#3) 
  3. Error: compile (@test_add_connected_constraints.R#12) 
  4. Error: (unknown) (@test_add_connected_constraints.R#3) 
  5. Error: compile (@test_add_connected_constraints.R#12) 
  6. Error: (unknown) (@test_add_connected_constraints.R#3) 
  7. Error: compile (@test_add_connected_constraints.R#12) 
  8. Error: (unknown) (@test_add_connected_constraints.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'run-all.R' [33s]
Running the tests in 'tests/run-all.R' failed.
Last 13 lines of output:
  Skipped:  0
  -- 1. Failure: ignored data files are not loaded (@test-load.R#183)  -----------
  `load.project(override.config = list(data_ignore = ""))` threw an error with unexpected message.
  Expected match: "file is encrypted or is not a database"
  Actual message: "file is not a database"
  
  WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
  WARNING: Perl module Spreadsheet::ParseXLSX cannot be loaded.
  WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
  == testthat results  ===========================================================
  OK: 637 SKIPPED: 4 FAILED: 1
  1. Failure: ignored data files are not loaded (@test-load.R#183) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'psychmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: correct_d
> ### Title: Correct _d_ values for range restriction and/or measurement
> ###   error
> ### Aliases: correct_d
> 
> ### ** Examples
> 
> ## Correction for measurement error only
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
    dgy   dgp   dGy   dGp
1 0.458 0.516 0.512 0.578
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = NULL, pa = .5, n1 = 100, n2 = 200)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
  value CI_LL_95 CI_UL_95   n n_effective
1 0.595      0.3    0.912 300         183
> 
> ## Correction for direct range restriction in the continuous variable
> correct_d(correction = "uvdrr_y", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)
Error in indirect_rr | rxxa_consistency : 
  operations are possible only for numeric, logical or complex types
Calls: correct_d -> correct_r -> correct_r_uvdrr
Execution halted
Authors@R field gives persons with no valid roles:
  Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see https://github.com/openjournals/joss-reviews/issues/470)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   2.4Mb
Error in re-building vignettes:
  ...
downloaded 0 bytes

Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot download all files
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    contrib   3.6Mb
    doc       2.9Mb
Running 'testthat.R' [130s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: new("dfm", x, docvars = data.frame(row.names = rownames(x)))
  13: initialize(value, ...)
  14: initialize(value, ...)
  15: callNextMethod()
  16: .nextMethod(.Object = .Object, ... = ...)
  17: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  18: asMethod(object, Class, value)
  19: slot(value, what)
  
  == testthat results  ===========================================================
  OK: 1938 SKIPPED: 27 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: new("dfm", x, docvars = data.frame(row.names = rownames(x)))
  13: initialize(value, ...)
  14: initialize(value, ...)
  15: callNextMethod()
  16: .nextMethod(.Object = .Object, ... = ...)
  17: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  18: asMethod(object, Class, value)
  19: slot(value, what)
  
  == testthat results  ===========================================================
  OK: 1938 SKIPPED: 27 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'tests.R' [1s]
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > op.warn <- getOption("warn")
  > options(warn = 2)
  > quantmod::getSymbols("SPY", src = "google", from = Sys.Date() - 10)
  '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.
  Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  : 
    (converted from warning) cannot open URL 'http://finance.google.com/finance/historical?q=SPY&startdate=Mar+24,+2018&enddate=Apr+03,+2018&output=csv': HTTP status was '403 Forbidden'
  Calls: <Anonymous> -> do.call -> getSymbols.google -> download.file
  Execution halted
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.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  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
'library' or 'require' call to 'FrF2.catlg128' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
    po    2.1Mb
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
Running examples in 'RCzechia-Ex.R' failed
The error most likely occurred in:

> ### Name: kraje
> ### Title: Regions (kraje) of the Czech Republic
> ### Aliases: kraje
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3
> 
> hranice <- kraje()
Error: unknown input format
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  -- 1. Error: (unknown) (@test-jla.R#6)  ----------------------------------------
  unknown input format
  1: expect_that(is.data.frame(republika()), is_true()) at testthat/test-jla.R:6
  2: condition(object)
  3: expect_true(x)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: is.data.frame(republika())
  7: republika()
  8: readRDS(url(remote_df))
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-jla.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'rsolr'
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'RgoogleMaps-Ex.R' failed
The error most likely occurred in:

> ### Name: GetMap.bbox
> ### Title: GetMap bbox
> ### Aliases: GetMap.bbox
> 
> ### ** Examples
> 
>  mymarkers <- cbind.data.frame(lat = c(38.898648,38.889112, 38.880940), 
+           lon = c(-77.037692, -77.050273, -77.03660), size =  c('tiny','tiny','tiny'), 
+           col = c('blue', 'green', 'red'), char = c('','',''));
> 
> ##get the bounding box:
>   bb <- qbbox(lat = mymarkers[,"lat"], lon = mymarkers[,"lon"]);
>   
> ##download the map:
>   MyMap <- GetMap.bbox(bb$lonR, bb$latR, destfile = "DC.png", GRAYSCALE =TRUE,
+                 markers = mymarkers);
>  ##The function qbbox() basically computes a bounding box for the given lat,lon 
>    #points with a few additional options such as quantile boxes, additional buffers, etc.  
>   bb <- qbbox(c(40.702147,40.711614,40.718217),c(-74.015794,-74.012318,-73.998284), 
+             TYPE = "all", margin = list(m=rep(5,4), TYPE = c("perc", "abs")[1]));
>  ##download the map:           
> MyMap <- GetMap.bbox(bb$lonR, bb$latR,destfile = "MyTile3.png", maptype = "satellite") 
Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.710182,-74.007039&zoom=15&size=640x640&maptype=satellite&format=png32&sensor=true': HTTP status was '403 Forbidden'
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=40.710182,-74.007039&zoom=15&size=640x640&maptype=satellite&format=png32&sensor=true'
Calls: GetMap.bbox -> GetMap -> download.file
Execution halted
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
.install_system_dependencies : <anonymous>: no visible global function
  definition for 'unzip'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'menu'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'download.file'
as.GParamSpec: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages required and available but unsuitable versions: 'grid' 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rmetasim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Rmpfr.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Authors@R field gives persons with no valid roles:
  Andrew MacDonald [rev] (Andrew MacDonald reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
  Andy  Teucher [rev] (Andy Teucher reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Scott Chamberlain [rev] (0000-0003-1444-9135)
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
Running 'test-all.R' [29s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  7: jsonlite::fromJSON(paste(get_base_url(), "tnrs/gnr/resolve?names=", taxa.string, 
         sep = ""))
  8: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  9: parseJSON(txt, bigint_as_char)
  10: parse_con(txt, bigint_as_char)
  11: open(con, "rb")
  12: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Resolving names with GNR works (@test_resolver.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Warning in self$configPolyhedraSource(source.config = sources.config[[source]],  :
  bytecode version mismatch; using eval

A namespace must be able to be loaded with just the base namespace
loaded: otherwise if the namespace gets loaded by a saved object, the
session will be unable to start.

Probably some imports need to be declared in the NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running examples in 'RSMET-Ex.R' failed
The error most likely occurred in:

> ### Name: meteofranceSynop
> ### Title: SYNOP Weather Data in France
> ### Aliases: meteofranceSynop
> 
> ### ** Examples
> 
>  
> 
> library(ggmap)
Loading required package: ggplot2
> data(meteofranceSynop)
> 
> 
> 
> 
> data=meteofranceSynop[meteofranceSynop$timestamp==meteofranceSynop$timestamp[250],]
> 
> 
> 
> map <- get_map(location ="France", zoom = 6)
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=France&zoom=6&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=France&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "France"
Error in data.frame(ll.lat = ll[1], ll.lon = ll[2], ur.lat = ur[1], ur.lon = ur[2]) : 
  arguments imply differing number of rows: 0, 1
Calls: get_map -> get_googlemap -> data.frame
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.Rcheck/00install.out' for details.
Running 'testthat.R' [347s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [417s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsunlight.Rcheck/00install.out' for details.
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 3.3.0 beta (2016-04-13 r70476)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

locale:
[1] LC_COLLATE=C                 LC_CTYPE=German_Germany.1252
[3] LC_MONETARY=C                LC_NUMERIC=C                
[5] LC_TIME=C                   

attached base packages:
[1] stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Authors@R field gives persons with no valid roles:
  ERC Grant Agreement number 336167 - the CHAI Project [fnd]
  Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
  Kara  Woo [rev] (Kara Woo reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
Package required and available but unsuitable version: 'RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/s2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/selectiveInference.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Entries with different classification: 1 (0.1%)
  Correlation between scores of matching entries: 0.5
  Average sentiment: 0.25 vs -0.4
  -- 1. Failure: dictionary generations works correctly (@test.generateDictionary.
  dictionary$scores not equal to c(-0.4190744, 0.3955698).
  2/2 mismatches (average diff: 0.0711)
  [1] -0.344 - -0.419 == 0.0746
  [2]  0.463 -  0.396 == 0.0675
  
  == testthat results  ===========================================================
  OK: 386 SKIPPED: 0 FAILED: 1
  1. Failure: dictionary generations works correctly (@test.generateDictionary.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
File 'sequoia/libs/i386/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.o'
File 'sequoia/libs/x64/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.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.
Authors@R field gives persons with no valid roles:
  Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1)
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Running CCA
  Computing nearest neighbor graph
  Computing SNN
  == testthat results  ===========================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_preprocessing.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [41s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  [1] "Scaling data matrix"
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |======================================================================| 100%
  Running CCA
  Computing nearest neighbor graph
  Computing SNN
  == testthat results  ===========================================================
  OK: 232 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_preprocessing.R#128) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: D:/temp/RtmpCowpeK/R.INSTALL1b7207d1d3c8f/sharpr2/man/sharpr2-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/sharpr2.Rcheck/00install.out' for details.
prepare_Rd: sharpr2-package.Rd:1: All text must be in a section
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   6.2Mb
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    |============================                                          |  40%
    |                                                                            
    |==========================================                            |  60%[1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  230769"
  [1] "Estimated replications per hour:  2307697"
  [1] "Estimated replications per hour:  256412"
  [1] "Estimated replications per hour:  2307838"
  [1] "Estimated replications per hour:  256412"
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 0 FAILED: 1
  1. Failure: summary.fun can handel logical data and returning vector 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test_scripts.R' [26s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in eval(expr, envir, enclos) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
contact_matrix: possible error in xtabs(data = contacts.sample, formula
  = weight ~ agegroup + cnt.agegroup, addNA = TRUE): unused argument
  (addNA = TRUE)
contact_matrix: possible error in xtabs(data = part.sample, formula =
  weight ~ agegroup, addNA = TRUE): unused argument (addNA = TRUE)
Running examples in 'socialmixr-Ex.R' failed
The error most likely occurred in:

> ### Name: contact_matrix
> ### Title: Generate a contact matrix from diary survey data
> ### Aliases: contact_matrix
> 
> ### ** Examples
> 
> data(polymod)
> contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 1, 5, 15))
Using Polymod Social Contact Data. To cite this in a publication, use the 'cite' function
Sampling the age of contacts with missing age from other participants of the same age group.
  To change this behaviour, set the 'missing.contact.age' option
Error in xtabs(data = contacts.sample, formula = weight ~ agegroup + cnt.agegroup,  : 
  unused argument (addNA = TRUE)
Calls: contact_matrix -> xtabs
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    @Misc{,
      title = {Polymod Social Contact Data},
      author = {Joël Mossong and Niel Hens and Mark Jit and Philippe Beutels and Kari Auranen and Rafael Mikolajczyk and Marco Massari and Stefania Salmaso and Gianpaolo Scalia Tomba and Jacco Wallinga and Janneke Heijne and Malgorzata Sadkowska-Todys and Magdalena Rosinska and W. John Edmunds},
      doi = {10.5281/zenodo.1059920},
      publisher = {Zenodo},
      note = {Version 1.1},
      year = {2017},
    }
  
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-matrix.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 57-58 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unused argument (addNA = TRUE)
Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sparsesvd.Rcheck/00install.out' for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.2Mb
Warning: invalid input found on input connection 'stability-Ex.R'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
Running examples in 'stocks-Ex.R' failed
The error most likely occurred in:

> ### Name: twometrics_graph
> ### Title: Graph One Performance Metric vs. Another for Various Investments
> ### Aliases: twometrics_graph
> 
> ### ** Examples
> 
> # Plot annualized growth vs. maximum drawdown for VFINX, SSO, and UPRO
> fig <- twometrics_graph(tickers = c("VFINX", "SSO", "UPRO"))
Error in 1:loc.end : argument of length 0
Calls: twometrics_graph -> load_gains
Execution halted
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

LaTeX errors:
! LaTeX Error: File `dirtytalk.sty' not found.

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

Execution halted
Authors@R field gives persons with no valid roles:
  Scott  Chamberlin [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Running examples in 'survtmle-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in `colnames<-`(`*tmp*`, value = c("t", "group", "value")) : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
Package suggested but not available for checking: 'tidyquant'
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 11
  1. Error: (unknown) (@test_sw_sweep.R#3) 
  2. Error: (unknown) (@test_tidiers_StructTS.R#3) 
  3. Error: (unknown) (@test_tidiers_arima.R#3) 
  4. Error: (unknown) (@test_tidiers_bats_tbats.R#3) 
  5. Error: (unknown) (@test_tidiers_decomposed_ts.R#3) 
  6. Error: (unknown) (@test_tidiers_ets.R#3) 
  7. Error: (unknown) (@test_tidiers_hw.R#3) 
  8. Error: (unknown) (@test_tidiers_lm.R#3) 
  9. Error: (unknown) (@test_tidiers_nnetar.R#3) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-30 (SW00_Introduction_to_sweep.Rmd) 
Error: processing vignette 'SW00_Introduction_to_sweep.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
Packages required and available but unsuitable versions:
  'parallel' 'phyloseq' 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  Luke Winslow [rev] (Reviewed for rOpenSci)
  Laura DeCicco [rev] (Reviewed for rOpenSci)
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'alphavantager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running examples in 'timetk-Ex.R' failed
The error most likely occurred in:

> ### Name: tk_augment_timeseries
> ### Title: Augment the time series signature to the data
> ### Aliases: tk_augment_timeseries tk_augment_timeseries_signature
> 
> ### ** Examples
> 
> library(tidyquant)
Error in library(tidyquant) : there is no package called 'tidyquant'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 9
  1. Error: (unknown) (@test_tk_augment_timeseries.R#2) 
  2. Error: (unknown) (@test_tk_get_timeseries.R#2) 
  3. Error: (unknown) (@test_tk_index.R#3) 
  4. Error: (unknown) (@test_tk_make_future_timeseries.R#2) 
  5. Error: (unknown) (@test_tk_tbl.R#6) 
  6. Error: (unknown) (@test_tk_ts.R#4) 
  7. Error: (unknown) (@test_tk_xts.R#4) 
  8. Error: (unknown) (@test_tk_zoo.R#4) 
  9. Error: (unknown) (@test_tk_zooreg.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-29 (TK00_Time_Series_Coercion.Rmd) 
Error: processing vignette 'TK00_Time_Series_Coercion.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Package required but not available: 'rsolr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'Coxph-Ex.R' [3s]
Running the tests in 'tests/Coxph-Ex.R' failed.
Complete output:
  > 
  > library("tram")
  Loading required package: mlt
  Loading required package: basefun
  Loading required package: variables
  > library("survival")
  > library("trtf")
  Error in library("trtf") : there is no package called 'trtf'
  Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'TH.data'

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

    geyser

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'quantreg'

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

    untangle.specials

Quitting from lines 22-51 (tram.Rnw) 
Error: processing vignette 'tram.Rnw' failed with diagnostics:
there is no package called 'trtf'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/treethresh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 10 - 9 == 1
  
  -- 2. Failure: random content can be retrieved (@test_udapi.R#10)  -------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10 - 9 == 1
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uwIntroStats.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 15
  1. Failure: Variable importance (@test_iris.R#15) 
  2. Failure: Variable importance (@test_iris.R#18) 
  3. Failure: OOB erros of nested models (@test_iris.R#25) 
  4. Failure: OOB erros of nested models (@test_iris.R#28) 
  5. Failure: Thresholds for the 3 steps (@test_iris.R#34) 
  6. Failure: Thresholds for the 3 steps (@test_iris.R#36) 
  7. Failure: Thresholds for the 3 steps (@test_iris.R#38) 
  8. Failure: Variable importance (@test_orange.R#16) 
  9. Failure: Variable importance (@test_orange.R#20) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  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  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'WufooR-Ex.R' failed
The error most likely occurred in:

> ### Name: fields_info
> ### Title: Return details about form's fields
> ### Aliases: fields_info
> 
> ### ** Examples
> 
> fields_info(formIdentifier = "z5kqx7h1gtvg4g", showRequestURL = TRUE)
Error in http_statuses[[as.character(status)]] : subscript out of bounds
Calls: fields_info -> doRequest -> stop_for_status
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: stop_for_status(getResponse)
  4: stop(http_condition(x, "error", task = task, call = call))
  5: http_condition(x, "error", task = task, call = call)
  6: http_status(status)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 5
  1. Error: Fields request returns 17 rows, always (@test-fieldsAndreports.R#9) 
  2. Error: Reports have 11 fields (@test-fieldsAndreports.R#16) 
  3. Error: Form request returns 17 rows, always (@test-forms.R#9) 
  4. Error: Form returns entries, with the requested URL (@test-forms.R#14) 
  5. Error: User request returns 17 rows, always (@test-users.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-47 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/WVPlots.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'GenomicScores'
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "# ç\u008f¾è¡ã\u0081®å­¦æ ¡ææ³ã\u0081§ã\u0081¯ã\u0081è±èªã\u0081«ã\
  y[1]: u0081ããã\u0081ã\u0081ªãç®çèªã\u008dãè£èªã\u008d"
  
  -- 2. Failure: UTF-8 is OK (@test.R#78)  ---------------------------------------
  length(op) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: UTF-8 is OK (@test.R#66) 
  2. Failure: UTF-8 is OK (@test.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
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'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/xptr.Rcheck/00install.out' for details.
Running examples in 'yCrypticRNAs-Ex.R' failed
The error most likely occurred in:

> ### Name: annotationsSet
> ### Title: Create a geneAnnotation object.
> ### Aliases: annotationsSet
> 
> ### ** Examples
> 
> annotationsSet()
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  scerevisiae_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: annotationsSet -> <Anonymous> -> useDataset
Execution halted