installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="webshotb6d773c33674.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb6d773c33674.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Package unavailable to check Rd xrefs: ‘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, basename, cbind, colMeans, colSums, colnames,
    dirname, 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: 1.42 secs
Identifing all possible orderings..
Total run time: 0.88 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]="webshotaa8d67b04631.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotaa8d67b04631.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
Error in re-building vignettes:
  ...
2020-02-22 02:44:55 INFO:: total elpsd: 5.5 secs | 1.417 caribouMovement move 5
2020-02-22 02:44:55 INFO:: total elpsd: 5.5 secs | 1.417 caribouMovement plot 10
2020-02-22 02:44:55 INFO:: total elpsd: 5.7 secs | 1.5 caribouMovement move 5
2020-02-22 02:44:55 INFO:: total elpsd: 5.7 secs | 1.5 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 5.8 secs | 1.583 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 5.8 secs | 1.583 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 6 secs | 1.667 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 6 secs | 1.667 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 6.1 secs | 1.75 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.2 secs | 1.75 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 6.3 secs | 1.833 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.3 secs | 1.833 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 6.4 secs | 1.917 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.5 secs | 1.917 caribouMovement plot 10
2020-02-22 02:44:56 INFO:: total elpsd: 6.6 secs | 2 fireSpread burn 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.6 secs | 2 caribouMovement move 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.6 secs | 2 fireSpread stats 5
2020-02-22 02:44:56 INFO:: total elpsd: 6.6 secs | 2 caribouMovement plot 10
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades() call.
Quitting from lines 386-390 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    libs  30.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.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
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spatialEco.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   9.4Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.8Mb
installed size is 18.1Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   8.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/speech.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sperich.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spfrontier.Rcheck/00install.out’ for details.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/splithalfr.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [149s/149s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(SPOT)
  > 
  > options(spot.run.full.test = F)
  > 
  > test_check("SPOT")
  ── 1. Failure: check that infillExpectedImprovement has same result as target=ei
  !all(resA$x == resC$x) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: check that infillExpectedImprovement has same result as target=ei (@test.infillExpectedImprovement.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.5Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.6Mb
Package required and available but unsuitable version: ‘grid’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ssr.Rcheck/00install.out’ for details.
No protocol specified

(R:27809): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:27817): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:27824): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:27831): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:27850): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:27873): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:27880): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:27887): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:27894): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:27904): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
  
  (R:27917): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
  No protocol specified
  Note: found 40588 marked UTF-8 strings
No protocol specified

(R:62442): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:62447): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:62452): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:62457): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:62474): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:62493): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:62498): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:62503): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:62508): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:62516): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.4Mb
Running ‘tinytest.R’ [29s/9s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  ----- FAILED[data]: test_codeMarkers.R<70--72>
   call| expect_equivalent(codeMarkers(gData = gData, removeDuplicates = FALSE, 
   call| impute = TRUE, imputeType = "random")$markers, matrix(c(0, 
   call| 0, 0, 1, 2, 0, 0, 0, 1, 1, 2, 0), nrow = 3))
   diff| Mean absolute difference: 1
  ----- FAILED[data]: test_codeMarkers.R<112--114>
   call| expect_equivalent(codeMarkers(gData = gData, MAF = 0.2, keep = "SNP1", 
   call| impute = FALSE)$markers, matrix(c(0, NA, 0, 0, NA, 1, 1, 
   call| 2, 0), nrow = 3))
   diff| 'is.NA' value mismatch: 2 in current 2 in target
  ----- FAILED[data]: test_codeMarkers.R<134--136>
   call| expect_equivalent(codeMarkers(gData = gData, refAll = "A", impute = FALSE)$markers, 
   call| matrix(c(2, NA, 2, 2, NA, 1, 1, 2, 0), nrow = 3))
   d
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/statgenSTA.Rcheck/00install.out’ for details.
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/STGS.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stormwindmodel.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.

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 213-217 (stplanr-od.Rmd) 
Error: processing vignette 'stplanr-od.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘BSgenome.Ptroglodytes.UCSC.panTro5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/StratigrapheR.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stream.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   9.1Mb
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package required but not available: ‘ShortRead’

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
sh: line 1: 13800 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/Rtmp3Fs7ok/x1335e058a2e03f/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x122fb2579
#1  0x122fb1945
#2  0x7fff93ac4529
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stUPscales.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/subgroup.discovery.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Surrogate.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  80.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   5.0Mb
Package suggested but not available for checking: ‘svHttp’
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.5Mb
Running examples in ‘tanaka-Ex.R’ failed
The error most likely occurred in:

> ### Name: tanaka
> ### Title: Plot a Tanaka Map
> ### Aliases: tanaka
> 
> ### ** Examples
> 
> library(tanaka)
> library(raster)
Loading required package: sp
> library(sf)
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
> com <- st_read(system.file("gpkg/com.gpkg", package = "tanaka"),
+                quiet = TRUE)
> ras <- raster(system.file("grd/elev.grd", package = "tanaka"))
> tanaka(ras)
> tanaka(ras, mask = com)
> tanaka(ras, breaks = seq(80,400,20),
+        legend.pos = "topright",
+        legend.title = "Elevation\n(meters)")
> tanaka(ras, nclass = 15,
+        col = hcl.colors(15, "YlOrRd"),
+        legend.pos = "topright",
+        legend.title = "Elevation\n(meters)")
Error in hcl.colors(15, "YlOrRd") : could not find function "hcl.colors"
Calls: tanaka -> plot -> plot.sfc_MULTIPOLYGON
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.4Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.2Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tensorsparse.Rcheck/00install.out’ for details.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Packages suggested but not available for checking:
  ‘lpsymphony’ ‘Rsymphony’ ‘gurobi’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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 80-86 (slickr.Rmd) 
Error: processing vignette 'slickr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘rsparse’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Package required but not available: ‘dipsaus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/thurstonianIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TideCurves.Rcheck/00install.out’ for details.
parse_dist.character : <anonymous>: no visible global function
  definition for ‘str2lang’
Undefined global functions or variables:
  str2lang
Running examples in ‘tidybayes-Ex.R’ failed
The error most likely occurred in:

> ### Name: lkjcorr_marginal
> ### Title: Marginal distribution of a single correlation from an LKJ
> ###   distribution
> ### Aliases: lkjcorr_marginal dlkjcorr_marginal plkjcorr_marginal
> ###   qlkjcorr_marginal rlkjcorr_marginal
> 
> ### ** Examples
> 
> 
> library(dplyr)

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

> library(ggplot2)
> 
> data.frame(prior = "lkjcorr_marginal(2, 3)") %>%
+   parse_dist(prior) %>%
+   ggplot(aes(y = prior, dist = .dist, args = .args)) +
+   stat_dist_halfeyeh() +
+   xlim(-1, 1) +
+   xlab("Marginal correlation for LKJ(3) prior on 2x2 correlation matrix")
Error: Discrete value supplied to continuous scale
Execution halted
Running ‘testthat.R’ [118s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. scales[[i]][[method]](data[[var]][scale_index[[i]]])
   19. ggplot2:::f(..., self = self)
   20. self$range$train(x)
   21. ggplot2:::f(..., self = self)
   22. scales::train_continuous(x, self$range)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 329 | SKIPPED: 124 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: geom aesthetic documention generator works (@test.geom.R#11) 
  2. Failure: parse_dist works on vectors (@test.parse_dist.R#13) 
  3. Failure: parse_dist works on data frames (@test.parse_dist.R#23) 
  4. Error: parse_dist + marginalize_lkjcorr produces correct results (@test.parse_dist.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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

Loading required package: ggplot2
Loading required package: maps
Loading required package: ggrepel
Warning in FUN(X[[i]], ...) : No results found for "Fake Address".
Quitting from lines 62-64 (tidygeocoder.Rmd) 
Error: processing vignette 'tidygeocoder.Rmd' failed with diagnostics:
cannot open URL 'http://nominatim.openstreetmap.org/search?q=Nairobi,+Kenya&format=xml&polygon=0&addressdetails=0'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tidyHeatmap.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:purrr':

    compose, simplify

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

    as_data_frame, groups, union

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

    as_data_frame

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

    decompose, spectrum

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

    union

Loading required package: viridisLite
Quitting from lines 123-124 (visualizing-json.Rmd) 
Error: processing vignette 'visualizing-json.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tidyrules.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tidyUSDA.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
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 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 685 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
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/3.5/tkrplot.Rcheck/00install.out’ for details.
Warning: loading Rplot failed

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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tkRplotR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tlrmvnmvt.Rcheck/00install.out’ for details.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  27.1Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tolerance.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.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

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

Package suggested but not available for checking: ‘PharmacoGx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs      9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tree.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/treespace.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

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

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



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 137-139 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-65 (structuredCoalescent.Rmd) 
Error: processing vignette 'structuredCoalescent.Rmd' failed with diagnostics:
object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/trendsegmentR.Rcheck/00install.out’ for details.
installed size is 77.4Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  72.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/trinROC.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 23, 2018 11:16:19 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:20 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
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
Error in re-building vignettes:
  ...
Loading required package: TSdbi
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.util.Configuration init
INFO: No configuration found. Apply defaults.
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:29 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN%2BUSA%2BMEX.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tsfknn.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tsmp.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]="webshot1fa456f4a1be.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1fa456f4a1be.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TTAinterfaceTrendAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TukeyRegion.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘grDevices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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.
Quitting from lines 195-196 (NCA.Rmd) 
Error: processing vignette 'NCA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       22.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ungroup.Rcheck/00install.out’ for details.
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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: magic
Loading required package: abind

     PLEASE NOTE:  As of version 0.3-5, no degenerate (zero area) 
     regions are returned with the "Qt" option since the R 
     code removes them from the triangulation. 
     See help("delaunayn").


Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   5.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/UNPaC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/urlshorteneR.Rcheck/00install.out’ for details.
.open : <anonymous>: possible error in dQuote(height, c("", "px")[1]):
  unused argument (c("", "px")[1])
browse : <anonymous>: possible error in dQuote(height, c("", "px")[1]):
  unused argument (c("", "px")[1])
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  21.4Mb
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Packages required but not available: ‘GenomicAlignments’ ‘Rsamtools’

Packages required and available but unsuitable versions:
  ‘GenomicRanges’ ‘IRanges’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/vanddraabe.Rcheck/00install.out’ for details.
installed size is 120.8Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     119.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
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.

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

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]="webshoteaf72ee2e4d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshoteaf72ee2e4d.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

     P.A. Burrough, R.A. McDonnell, 1998. Principles of Geographical
     Information Systems. Oxford University Press.

     Stichting voor Bodemkartering (STIBOKA), 1970. Bodemkaart van
     Nederland : Blad 59 Peer, Blad 60 West en 60 Oost Sittard: schaal
     1 : 50 000. Wageningen, STIBOKA.

     <URL: http://www.gstat.org/>

_E_x_a_m_p_l_e_s:

     data(meuse)
     summary(meuse)
     coordinates(meuse) <- ~x+y
     proj4string(meuse) <- CRS("+init=epsg:28992")
     

Variable "l_cad" contains positive and negative values, so midpoint is set to 0. Set midpoint = NA to show the full spectrum of the color palette.
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
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.
Quitting from lines 135-144 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/vcvComp.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.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    doc    1.2Mb
    help   2.9Mb
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  53.3Mb
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘ggplot2’ in library.dynam(lib, package, package.lib):
 shared object ‘Rcpp.so’ not found
Execution halted
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WeibullFit.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
Package suggested but not available for checking: ‘org.Mm.eg.db’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/windAC.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...


Attaching package: 'plotly'

The following object is masked from 'package:ggplot2':

    last_plot

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

    filter

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

    layout

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]="webshotdf9e332da123.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotdf9e332da123.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wyz.code.metaTesting.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wyz.code.rdoc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wyz.code.testthat.Rcheck/00install.out’ for details.
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Packages suggested but not available for checking: ‘ChemmineR’ ‘fmcsR’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/xrnet.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/yager.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/yap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/yarr.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.
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   2.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ZipRadius.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [26s/40s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Loading required package: raster
  Loading required package: sp
  ── 1. Error: LoadModule works (@testLoadModule.R#15)  ──────────────────────────
  cannot open the connection
  Backtrace:
   1. base::write(...)
   2. base::cat(...)
   3. base::file(file, ifelse(append, "a", "w"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 201 | SKIPPED: 31 | WARNINGS: 10 | FAILED: 1 ]
  1. Error: LoadModule works (@testLoadModule.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Welcome to package ztable ver 0.2.0
Warning in engine$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 103-108 (ztable_update.Rmd) 
Error: processing vignette 'ztable_update.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
In addition: Warning message:
In engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted