installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rggobi.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/rgl.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  11.1Mb
    libs   9.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.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 40-46 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 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/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
  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/RHRV.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/Rirt.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/RISCA.Rcheck/00install.out’ for details.
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/rise.Rcheck/00install.out’ for details.
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.8Mb
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  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 use Fortran I/O
nor system RNGs. 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.
Package suggested but not available for checking: ‘golubEsets’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rLindo.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Error in re-building vignettes:
  ...
`type` used, `query` ignored.
Data retrieval 100%   
                                                                        
Found 12 interactions
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
Data retrieval 7.14%   
Data retrieval 14.3%   
Data retrieval 21.4%   
Data retrieval 28.6%   
Data retrieval 35.7%   
Data retrieval 42.9%   
Data retrieval 50%   
Data retrieval 57.1%   
Data retrieval 64.3%   
Data retrieval 71.4%   
Data retrieval 78.6%   
Data retrieval 85.7%   
Data retrieval 92.9%   
Data retrieval 100%   
                                                                        
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 251-258 (rmangal.Rmd) 
Error: processing vignette 'rmangal.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  25.5Mb
Running ‘testthat.R’ [108s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("RMixtCompIO")
  ── 1. Failure: functional model works (@test.run.R#324)  ───────────────────────
  rand.index(partition, resGen$z) is not more than 0.9. Difference: -0.0646
  
          partition
  zPredict 1 2
         1 0 3
         2 3 0
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: functional model works (@test.run.R#324) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rMouse.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/Rmpi.Rcheck/00install.out’ for details.
Packages required but not available: ‘Rata’ ‘Rirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 95.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     93.8Mb
Packages required and available but unsuitable versions:
  ‘impute’ ‘MassSpecWavelet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/robfilter.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘beadarrayExampleData’ ‘illuminaHumanv3.db’
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Package suggested but not available for checking: ‘Rglpk’
Package suggested but not available for checking: ‘ROI.plugin.glpk’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ROpenCVLite.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/ROracle.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.5Mb
S3 methods shown with full name in documentation object 'cbind.fill':
  ‘cbind.fill’

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  7.0Mb
  sub-directories of 1Mb or more:
    R       3.3Mb
    libs    2.0Mb
    tests   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpanel.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/RPEClust.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/rpg.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rpoppler.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  11: stringr::str_trim
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 8 FAILED: 1
  1. Error: thisfile works with knitr (@test-thisfile.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.8Mb
installed size is 76.2Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
Error in re-building vignettes:
  ...
Warning in engine$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
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

Loading required package: ggplot2
Quitting from lines 68-69 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
Execution halted
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. 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.
Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsparse.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 131.9Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     1.2Mb
    libs  128.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 230.3Mb
  sub-directories of 1Mb or more:
    libs  227.6Mb
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  12.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rsymphony.Rcheck/00install.out’ for details.
Running ‘run_test.R’ [8s/8s]
Running the tests in ‘tests/run_test.R’ failed.
Complete output:
  > all_files <- list.files("testthat",full.names=T,pattern="*.R$")
  > 
  > sapply(all_files,source)
  Loading required package: magick
  Linking to ImageMagick 6.9.9.39
  Enabled features: cairo, fontconfig, freetype, lcms, pango, rsvg, webp
  Disabled features: fftw, ghostscript, x11
  Loading required package: XML
  Error: Test failed: 'RTestCollection write HTML summary errors'
  * `writeExecSummary.html(...)` produced warnings.
  * `writeExecSummary.html(...)` produced warnings.
  Execution halted
Running ‘testthat.R’ [6s/6s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [6]  0.0394 -  0.0428 == -0.00345
  [7]  0.4000 -  0.0000 ==  0.40000
  [8]  0.6000 -  0.8000 == -0.20000
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 58 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
  1. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#36) 
  2. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#42) 
  3. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#77) 
  4. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#113) 
  5. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#119) 
  6. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#154) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot13a4b44c3aa91.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13a4b44c3aa91.png': No such file or directory
Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-26 (mcMat.Rmd) 
Error: processing vignette 'mcMat.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/RtmpztfoDx/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_67546969ee4c/sourceCpp_2.so':
  dlopen(/private/tmp/RtmpztfoDx/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_67546969ee4c/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/RtmpztfoDx/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_67546969ee4c/sourceCpp_2.so
  Reason: image not found
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.9Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     57.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs    6.3Mb
    yacas   1.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs    7.0Mb
    yacas   1.3Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SafeBayes.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.2Mb
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 50-51 (sass.Rmd) 
Error: processing vignette 'sass.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/sclr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   4.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SEERaBomb.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘flowMerge’ ‘flowClust’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/semEff.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/semnar.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-50 (simulate_rnaseq.Rmd) 
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
there is no package called 'airway'
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   7.2Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘SingleCellExperiment’ ‘MAST’ ‘rtracklayer’ ‘monocle’
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 159.3Mb
  sub-directories of 1Mb or more:
    doc      12.0Mb
    libs    143.2Mb
    sqlite    1.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.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/sglasso.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
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/shapes.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot1057065329cc7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1057065329cc7.png': No such file or directory
Quitting from lines 28-44 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘maftools’

Packages suggested but not available for checking:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.9Mb
Package required but not available: ‘BSgenome’

Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’

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

Packages suggested but not available for checking: ‘clipper’ ‘topologyGSA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  16.8Mb
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
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.

Execution halted
Package required but not available: ‘rosr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sivipm.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SLEMI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 132-133 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   8.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.3Mb
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sobir)
  > 
  > test_check("sobir")
  ── 1. Failure: perm_area should calculate the no-data zone areas for each permut
  bperm[7, 4] is not strictly less than 0.4. Difference: 0.0404
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: perm_area should calculate the no-data zone areas for each permutation of the data simulated nsim times (@tests.R#41) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  ...
Attaching package: 'RandomFields'

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

    RFoptions

Setting:
  options(
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    rasterTmpDir = '/private/tmp/RtmpA6jyhK/raster'
    reproducible.cachePath = '/private/tmp/RtmpA6jyhK/reproducible/cache'
    spades.inputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/inputs'
    spades.outputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/outputs'
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades() call.
Quitting from lines 376-380 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  30.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Running examples in ‘spatialEco-Ex.R’ failed
The error most likely occurred in:

> ### Name: sa.trans
> ### Title: Trigonometric transformation of a slope and aspect interaction
> ### Aliases: sa.trans
> 
> ### ** Examples
> 
>  sa.trans(slope = 48.146, aspect = 360.000)
[1] -0.2383874
> 
>  library(raster)
Loading required package: sp

Attaching package: ‘raster’

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

    shift

>  data(elev)
>  sa <- raster::terrain(elev, opt=c("slope", "aspect"), unit="degrees")

 *** caught segfault ***
address 0x11e989ff8, cause 'memory not mapped'

Traceback:
 1: .terrain(as.double(values(x)), as.integer(dim(out)), rs, un,     nopt, lonlat, y)
 2: .local(x, ...)
 3: raster::terrain(elev, opt = c("slope", "aspect"), unit = "degrees")
 4: raster::terrain(elev, opt = c("slope", "aspect"), unit = "degrees")
An irrecoverable exception occurred. R is aborting now ...
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   9.4Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.8Mb
uniquemap.matrix: no visible global function definition for ‘asplit’
Undefined global functions or variables:
  asplit
Running ‘testsAtoD.R’ [60s/60s]
Running the tests in ‘tests/testsAtoD.R’ failed.
Last 13 lines of output:
  +    if(!isTRUE(all.equal(u4, uc4)))
  +      stop("Inconsistency between algorithms in uniquemap.matrix")
  +    
  +    ## uniquemap.default
  +    a <- letters[c(1, 1:4, 3:2)]
  +    checkum(a, "<character>")
  +    checkum(as.list(a), "<list>")
  +    u1 <- uniquemap(a)
  +    u2 <- uniquemap(as.list(a))
  +    if(!isTRUE(all.equal(u1, u2)))
  +      stop("Inconsistency between algorithms in uniquemap.default")
  + })
  Error in asplit(x, 2) : could not find function "asplit"
  Calls: local ... eval -> eval -> checkum -> uniquemap -> uniquemap.matrix
  Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   8.4Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
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/splithalfr.Rcheck/00install.out’ for details.
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:52334): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:52341): 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:52348): 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:52355): 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:52374): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:52397): 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:52404): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:52411): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:52418): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:52428): 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:52441): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
  No protocol specified
  Note: found 40588 marked UTF-8 strings
Running ‘testthat.R’ [6s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  34: withOneRestart(expr, restarts[[1L]])
  35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  36: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  37: FUN(X[[i]], ...)
  38: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  39: force(code)
  40: doWithOneRestart(return(expr), restart)
  41: withOneRestart(expr, restarts[[1L]])
  42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  43: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  45: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  46: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  47: test_check("stacomiR")
  An irrecoverable exception occurred. R is aborting now ...
Packages required and available but unsuitable versions: ‘tergm’ ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required and available but unsuitable versions:
  ‘groupedstats’ ‘MCMCpack’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'SuperGauss-quicktut.Rmd' failed with diagnostics:
there is no package called 'stringi'
Execution halted
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SuppDists.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/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
Package suggested but not available for checking: ‘svHttp’
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/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
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 17.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  14.8Mb
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.
Packages required and available but unsuitable versions: ‘ergm’ ‘MASS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Quitting from lines 80-86 (slickr.Rmd) 
Error: processing vignette 'slickr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running examples in ‘threejs-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphjs
> ### Title: Interactive 3D Graph Visualization
> ### Aliases: graphjs
> 
> ### ** Examples
> 
> set.seed(1)
> g <- sample_islands(3, 10, 5/10, 1)
> i <- cluster_optimal(g)
Error in cluster_optimal(g) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Execution halted
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.
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
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’
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: ‘CoreGx’

Package suggested but not available for checking: ‘PharmacoGx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/TPMplt.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: 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
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 76.9Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  72.0Mb
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 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.
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

Loading required package: forecast
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]="webshot17f502de19e53.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17f502de19e53.png': No such file or directory
Quitting from lines 99-117 (TSplotly.Rmd) 
Error: processing vignette 'TSplotly.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.
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]="webshot1605266051148.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1605266051148.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.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
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
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WeibullFit.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
Package suggested but not available for checking: ‘org.Mm.eg.db’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/windAC.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wtss.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
guardExecution: no visible binding for global variable ‘errorCondition’
guardExecution: no visible binding for global variable
  ‘warningCondition’
offensiveProgrammingWrapFunction: no visible global function definition
  for ‘str2lang’
opwf: no visible global function definition for ‘str2lang’
Undefined global functions or variables:
  errorCondition str2lang warningCondition
Running examples in ‘wyz.code.metaTesting-Ex.R’ failed
The error most likely occurred in:

> ### Name: generateData
> ### Title: Generate Data
> ### Aliases: generateData
> ### Keywords: programation utilities
> 
> ### ** Examples
> 
> # typical example
> op_sum <- opwf(sum, c('...', 'removeNA_b_1'))
Error in str2lang(bd) : could not find function "str2lang"
Calls: opwf
Execution halted
Running ‘testthat.R’ [9s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 414 | SKIPPED: 0 | WARNINGS: 7 | FAILED: 12 ]
  1. Error: (unknown) (@test_exploreSignatures.R#3) 
  2. Error: (unknown) (@test_generateData.R#3) 
  3. Error: guardExecution - coverage (@test_guardExecution.R#8) 
  4. Failure: opfw - good cases (@test_opwf.R#38) 
  5. Failure: opfw - good cases (@test_opwf.R#39) 
  6. Failure: opfw - good cases (@test_opwf.R#43) 
  7. Failure: opfw - good cases (@test_opwf.R#44) 
  8. Failure: opfw - good cases (@test_opwf.R#48) 
  9. Failure: opfw - good cases (@test_opwf.R#49) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
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 34.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
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’ [27s/65s]
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