Packages suggested but not available for checking: 'rgl', 'FRB'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HeritSeq.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  15.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr
Quitting from lines 434-443 (hetGP_vignette.Rnw) 
Error: processing vignette 'hetGP_vignette.Rnw' failed with diagnostics:
invalid 'z' limits
--- failed re-building ‘hetGP_vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘hetGP_vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiCfeat.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HierO.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   1.3Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.0Mb
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/3.6/hiPOD.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘trackr’
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/3.6/HiveR.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.3Mb
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/3.6/hmgm.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘Rcpp’ ‘methods’ ‘rgl’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hoardeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'iheatmapr', 'ropls'
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulating-data.Rmd’ using rmarkdown
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 25-31 (simulating-data.Rmd) 
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
there is no package called 'ropls'
--- failed re-building ‘simulating-data.Rmd’

SUMMARY: processing the following file failed:
  ‘simulating-data.Rmd’

Error: Vignette re-building failed.
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/3.6/homals.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
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 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hpackedbubble.Rmd’

SUMMARY: processing the following file failed:
  ‘hpackedbubble.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘hpa/libs/hpa.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  'RGtk2', 'cairoDevice', 'RGtk2Extras'
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HSAR.Rcheck/00install.out’ for details.
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
Running ‘testthat.R’ [51s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   24. base:::withOneRestart(expr, restarts[[1L]])
   25. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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/3.6/HUM.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
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 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building failed.
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/3.6/hyper.fit.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘flowCore’
Error loading dataset 'Samusik_01_subset':
   Error in .requirePackage(package) : 
    unable to find required package 'flowCore'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
Running examples in ‘hyperSpec-Ex.R’ failed
The error most likely occurred in:

> ### Name: hy.unittest
> ### Title: hyperSpec unit tests
> ### Aliases: hy.unittest
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> 
> hy.unittest ()
all_wl: .......
wc: wc: illegal option -- -
usage: wc [-clmw] [file ...]
Warning in system("wc --help", intern = TRUE) :
  running command 'wc --help' had status 1
Error: Reason: wc not available
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/3.6/hypervolume.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ibmsunburst.Rmd’

SUMMARY: processing the following file failed:
  ‘ibmsunburst.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ICAMS.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
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 84-88 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   5.9Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Package suggested but not available for checking: ‘mixAK’
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> data("world20")
> y=na.omit(diff(log(world20[,1])))
> 
> ## Simulation data
> #dat=rnorm(200,5,1)
> #y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
  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/3.6/icosa.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.2Mb
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  63.2Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.7Mb
Error(s) in re-building vignettes:
--- re-building ‘model_details.Rmd’ using rmarkdown
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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
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 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
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.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  14.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     18.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
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 87-89 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
--- failed re-building ‘getstarted.Rmd’

SUMMARY: processing the following file failed:
  ‘getstarted.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: 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/3.6/Immigrate.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.3Mb
Packages suggested but not available for checking: 'rsprng', 'Rmpi'
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 98578 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmphJ1oqo/x131810a3772ae5f/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmphJ1oqo/x131810a3772ae5f/iofile -n -s 2>/dev/null' had status 133
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/3.6/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/3.6/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  0x12c91e579
#1  0x12c91d945
#2  0x7fff9a10b529
Error: 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
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Packages suggested but not available for checking:
  'MLP', 'org.Hs.eg.db', 'a4Base'
Error(s) in re-building vignettes:
--- re-building ‘IntGraphTutorial.Rmd’ using rmarkdown
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: 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

Loading required package: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Loading required package: gtools
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]="webshot15a63ac4ea79.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15a63ac4ea79.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘IntGraphTutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘IntGraphTutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘apeglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.0Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘flush.console’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  flush.console lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ionflows.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
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.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
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: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/8]
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'pcalg'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          14.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/JFE.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/jomo.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Missing or unexported object: ‘tidyr::unnest_legacy’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.6Mb
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/3.6/kernhaz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Hs.eg.db’
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/3.6/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmcudaR.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/3.6/kml3d.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/3.6/kml.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/3.6/kmlShape.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.3Mb
Error(s) in re-building vignettes:
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
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: '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

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘copper_mining_2d.Rmd’

--- re-building ‘ordinary_kriging.Rmd’ using rmarkdown
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.
--- finished re-building ‘ordinary_kriging.Rmd’

--- re-building ‘simple_kriging.Rmd’ using rmarkdown
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.
--- finished re-building ‘simple_kriging.Rmd’

--- re-building ‘universal_kriging.Rmd’ using rmarkdown
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.
--- finished re-building ‘universal_kriging.Rmd’

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘kstIO.Rnw’ using Sweave
Loading required package: pks
Loading required package: sets
Loading required package: MASS
Loading required package: stringr

Attaching package: ‘stringr’

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

    %>%

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 1 
Error in library("kst") : there is no package called ‘kst’

--- failed re-building ‘kstIO.Rnw’

SUMMARY: processing the following file failed:
  ‘kstIO.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rgraphviz’
Error(s) in re-building vignettes:
--- re-building ‘kst.Rnw’ using Sweave
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error: processing vignette 'kst.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘kst.Rnw’

SUMMARY: processing the following file failed:
  ‘kst.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LambertW.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LANDD.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is 144.2Mb
  sub-directories of 1Mb or more:
    libs  142.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
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 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_lavaanPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'Rgraphviz', 'graph'
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/3.6/lba.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lda.svi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/leapp.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.4Mb
Packages suggested but not available for checking: 'gWidgetsRGtk2', 'RGtk2'
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Understanding_lime.Rmd’

SUMMARY: processing the following file failed:
  ‘Understanding_lime.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.8Mb
    testdata   1.6Mb
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/3.6/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error in ls.problem(model.text.lsp) : 
  has.localsolver(ls.path) is not TRUE
Calls: ls.problem -> stopifnot
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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/3.6/longitudinalData.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/loon.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LoopRig.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [11s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 147 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#29) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#40) 
  
  Error: testthat unit tests failed
  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/3.6/LOST.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   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/3.6/LSAfun.Rcheck/00install.out’ for details.
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.3Mb
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: ICtree
> ### Title: Fit a survival tree for interval-censored survival data
> ### Aliases: ICtree
> 
> ### ** Examples
> 
> library(interval)
Error in library(interval) : there is no package called ‘interval’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
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 min(diff(sort(ux))) :
  no non-missing arguments to min; returning Inf
Quitting from lines 199-207 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
there is no package called 'interval'
--- failed re-building ‘LTRCtrees.Rmd’

SUMMARY: processing the following file failed:
  ‘LTRCtrees.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
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 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘LUCIDus-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘LUCIDus-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.7Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
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/3.6/Maeswrap.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: interactive_blur (@test_interactive_blur.R#6) 
  2. Error: interactive_canny (@test_interactive_canny.R#5) 
  3. Error: interactive_charcoal (@test_interactive_charcoal.R#6) 
  4. Error: interactive_composite (@test_interactive_composite.R#5) 
  5. Error: interactive_despeckle (@test_interactive_despeckle.R#6) 
  6. Error: interactive_emboss (@test_interactive_emboss.R#6) 
  7. Error: interactive_implode (@test_interactive_implode.R#6) 
  8. Error: interactive_modulate (@test_interactive_modulate.R#6) 
  9. Error: interactive_oilpaint (@test_interactive_oilpaint.R#6) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  72.8Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.2Mb
Error(s) in re-building vignettes:
--- re-building ‘manhattanly.Rmd’ using rmarkdown
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: '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]="webshotd4a14dcd902a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd4a14dcd902a.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manhattanly.Rmd’

SUMMARY: processing the following file failed:
  ‘manhattanly.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
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]="webshot26c62068963e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot26c62068963e.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘manipulateWidgets.Rmd’

SUMMARY: processing the following file failed:
  ‘manipulateWidgets.Rmd’

Error: Vignette re-building failed.
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/3.6/maotai.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs         16.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mapmisc.Rnw’ using knitr
Loading required package: sp
Loading required package: raster
map images will be cached in  /tmp/Rtmpvjscv5/mapmiscCache
--- finished re-building ‘mapmisc.Rnw’

--- re-building ‘north.Rmd’ using docco_linear
Quitting from lines 221-238 (north.Rmd) 
Error: processing vignette 'north.Rmd' failed with diagnostics:
unable to find an inherited method for function 'coordinates' for signature '"numeric"'
--- failed re-building ‘north.Rmd’

pandoc --self-contained --to=html5 --css=http://diseasemapping.r-forge.r-project.org/webpage.css --output=north.html north.md	
make: pandoc: No such file or directory
make: *** [north.html] Error 1
Error in tools:::buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mapmisc.Rcheck/vign_test/mapmisc",  : 
  running 'make' failed
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   7.9Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.6Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
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/3.6/mcca.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   8.3Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

> fitBernoulli <- mcemGLMM(fixed = Mate ~ 0 + Cross, 
+     random = list(~0 + Female, ~0 + Male), data = salamander, 
+     family = "bernoulli", vcD .... [TRUNCATED] 

Execution halted

... incomplete output.  Crash?
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 29.9Mb
  sub-directories of 1Mb or more:
    libs  28.8Mb
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   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/3.6/MDSMap.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/3.6/mdsOpt.Rcheck/00install.out’ for details.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Mega2R.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.6Mb
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking: 'clpAPI', 'ctc'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified

(R:50774): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50780): 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:50786): 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:50792): 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:50816): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50840): 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:50846): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50852): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50858): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50870): 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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
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 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
--- failed re-building ‘MetaIntegrator.Rmd’

--- re-building ‘MetaIntegratorRealExample.Rmd’ using rmarkdown_notangle
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.
--- finished re-building ‘MetaIntegratorRealExample.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaIntegrator.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetaPath.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GEOquery', 'affy', 'hgu133plus2.db', 'doSMP', 'impute'
Namespaces in Imports field not imported from:
  ‘CompQuadForm’ ‘lme4’
  All declared Imports should be used.
Packages suggested but not available for checking:
  'HTSFilter', 'DESeq', 'DESeq2'
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘metaRNASeq.Rnw’ using Sweave

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

--- failed re-building ‘metaRNASeq.Rnw’

SUMMARY: processing the following file failed:
  ‘metaRNASeq.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 77.8Mb
  sub-directories of 1Mb or more:
    libs  77.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs  17.3Mb
    misc   1.1Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  17.2Mb
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/3.6/MFHD.Rcheck/00install.out’ for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
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 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘structSSI’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Running ‘testthat.R’ [50s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ...
  
  ── 2. Failure: (unknown) (@test-sampleMiceObj.R#22)  ───────────────────────────
  `moComp` not equal to `smComp`.
  Component "Dataset_1": Column 'Petal.Width': Mean relative difference: 0.1333333
  Component "Dataset_2": Column 'Petal.Width': Mean relative difference: 0.1052632
  Component "Dataset_3": Column 'Petal.Width': Mean relative difference: 0.1666667
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: (unknown) (@test-sampleMiceObj.R#18) 
  2. Failure: (unknown) (@test-sampleMiceObj.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [20s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘paper.Rnw’ using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘paper.Rnw’

Error: Vignette re-building failed.
Execution halted
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Error(s) in re-building vignettes:
--- re-building ‘milr-intro.Rmd’ using rmarkdown
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.
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL 'http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz'
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.

Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.9Mb
Packages suggested but not available for checking: 'mixAK', 'BRugs'
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/missDeaths.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mixKernel.Rcheck/00install.out’ for details.
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

> ### Name: mixsiar_gui
> ### Title: Run the GUI version of MixSIAR
> ### Aliases: mixsiar_gui
> 
> ### ** Examples
> 
> mixsiar_gui()
Error in mixsiar_gui() : 
  *** gWidgetsRGtk2 package not able to be loaded. ***
        If 'library('gWidgetsRGtk2')' does not work, MixSIAR GUI will not run.
        On Windows/Linux, try 'install.packages('gWidgetsRGtk2')'.
        On Mac, close R, download and install GTK+ from:
        http://r.research.att.com/#other. Then install latest X11 application
        (xQuartz) from http://xquartz.macosforge.org/landing/.

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
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.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 png::readPNG(path, native = TRUE, info = TRUE) :
  libpng warning: iCCP: CRC error
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   2.3Mb
    help   1.5Mb
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
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/3.6/MMDai.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Package required but not available: ‘doMPI’

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/3.6/molaR.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Packages required but not available: 'org.Hs.eg.db', 'clusterProfiler'

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/3.6/morphomap.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.2Mb
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
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 342-344 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
--- failed re-building ‘tutorial.Rmd’

--- re-building ‘modelling.Snw’ using Sweave
--- finished re-building ‘modelling.Snw’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.0Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘Biostrings’
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
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 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msaR.Rmd’

SUMMARY: processing the following file failed:
  ‘msaR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  37.0Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
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]="webshot127825d88bea8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot127825d88bea8.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

SUMMARY: processing the following file failed:
  ‘msir.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSIseq.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/3.6/MSQC.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  16.2Mb
Running examples in ‘mssqlR-Ex.R’ failed
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/3.6/mtk.Rcheck/00install.out’ for details.
Packages required but not available:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 83.5Mb
  sub-directories of 1Mb or more:
    libs  83.3Mb
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x10f5b2262, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  32: withOneRestart(expr, restarts[[1L]])
  33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  34: 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()    })
  35: FUN(X[[i]], ...)
  36: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  37: force(code)
  38: doWithOneRestart(return(expr), restart)
  39: withOneRestart(expr, restarts[[1L]])
  40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  41: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: 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)
  44: 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)
  45: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mvgraphnorm.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/3.6/mvmesh.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
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.
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

SUMMARY: processing the following file failed:
  ‘vignette_mvord.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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/3.6/nat.nblast.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/3.6/nat.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/3.6/nat.templatebrains.Rcheck/00install.out’ for details.
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.1Mb
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/3.6/NeatMap.Rcheck/00install.out’ for details.
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘netgsa.Rmd’ using rmarkdown
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 86-89 (netgsa.Rmd) 
Error: processing vignette 'netgsa.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘netgsa.Rmd’

SUMMARY: processing the following file failed:
  ‘netgsa.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.4Mb
Packages suggested but not available for checking:
  'limma', 'DESeq2', 'edgeR', 'org.Hs.eg.db'
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/3.6/neuroim.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
--- re-building ‘NFP.Rmd’ using rmarkdown
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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: graphite
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘NFP.Rmd’

SUMMARY: processing the following file failed:
  ‘NFP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 35.4Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.0Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          19.0Mb
    tests          1.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NIPTeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nlcv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
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 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocode.Rmd’

SUMMARY: processing the following file failed:
  ‘geocode.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  clang-7: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nloptr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'doMPI', 'Biobase'
Error loading dataset 'esGolub':
   Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMF-vignette.Rnw’ using knitr
Quitting from lines 385-398 (NMF-vignette.Rnw) 
Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
unable to find required package 'Biobase'
--- failed re-building ‘NMF-vignette.Rnw’

--- re-building ‘heatmaps.Rnw’ using knitr
Converted 2 of 2 package citations to BibTeX
Writing 4 Bibtex entries ... OK
Results written to file 'Rpackages.bib'
--- finished re-building ‘heatmaps.Rnw’

SUMMARY: processing the following file failed:
  ‘NMF-vignette.Rnw’

Error: Vignette re-building failed.
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/3.6/NNS.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/3.6/nonlinearTseries.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
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/3.6/NPCirc.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘PMA’
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  16.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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.

See ‘Writing portable packages’ 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/3.6/OceanView.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.6Mb
    libs   3.0Mb
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/3.6/OCNet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
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/3.6/onemap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ontologyPlot’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenCL.Rcheck/00install.out’ for details.
installed size is 74.7Mb
  sub-directories of 1Mb or more:
    libs   64.9Mb
    share   9.7Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   6.0Mb
installed size is 187.3Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    177.2Mb
    models    4.6Mb
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/3.6/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Packages suggested but not available for checking:
  'gurobi', 'ggtree', 'Rsymphony', 'lpsymphony'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package unavailable to check Rd xrefs: ‘ggtree’
Packages suggested but not available for checking:
  'GO.db', 'org.At.tair.db'
Running ‘bdstest.R’ [2s/4s]
  Running ‘hobbs.R’ [5s/14s]
Running the tests in ‘tests/hobbs.R’ failed.
Last 13 lines of output:
  In kktchk(ans$par, fn, wgr, hess = NULL, upper = NULL, lower = NULL,  :
    Eigenvalue failure for projected Hessian
  This problem is unconstrained.
  Error in lbfgsb3::lbfgsb3(prm = spar, fn = efn, gr = egr, control = mcontrol,  : 
    NA/NaN/Inf in foreign function call (arg 7)
  In addition: Warning messages:
  1: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  2: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  3: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  4: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  libc++abi.dylib: terminating with uncaught exception of type std::range_error: non-finite x values not allowed in calfun
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/3.6/optiSel.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.7Mb
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/3.6/optiSolve.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘graph’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Packages suggested but not available for checking: 'IsoGene', 'Biobase'
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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.

See ‘Writing portable packages’ 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/3.6/orthoDr.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
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.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
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.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
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 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
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.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
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.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
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.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
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 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PACVr.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘CorShrink’
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘evals.Rmd’ using rmarkdown
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 13-19 (evals.Rmd) 
Error: processing vignette 'evals.Rmd' failed with diagnostics:
package or namespace load failed for 'futile.logger' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'formatR'
--- failed re-building ‘evals.Rmd’

--- re-building ‘knitr.Rmd’ using rmarkdown
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.
--- finished re-building ‘knitr.Rmd’

--- re-building ‘pander.Rmd’ using rmarkdown
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

--- finished re-building ‘pander.Rmd’

--- re-building ‘pandoc_table.Rmd’ using rmarkdown
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.
--- finished re-building ‘pandoc_table.Rmd’

SUMMARY: processing the following file failed:
  ‘evals.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
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 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parcoords-.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-parcoords-.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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.

See ‘Writing portable packages’ 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/3.6/patternize.Rcheck/00install.out’ for details.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdPROF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdZMQ.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.7Mb
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/3.6/pca3d.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.1Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 108.0Mb
  sub-directories of 1Mb or more:
    doc     2.6Mb
    libs  105.0Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCGSE.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/3.6/PCRedux.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  11.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package suggested but not available for checking: ‘globaltest’
Found the following significant warnings:
  Warning: package ‘biomaRt’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PepPrep.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/permGPU.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocParallel’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data       2.3Mb
    examples   2.6Mb
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/phreeqc.Rcheck/00install.out’ for details.
installed size is 37.1Mb
  sub-directories of 1Mb or more:
    libs  36.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘phybreak_intro.Rmd’ using rmarkdown
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
Error(s) in re-building vignettes:
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
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]="webshotc4dc454c7107.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotc4dc454c7107.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
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 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
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/3.6/phylocurve.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.3Mb
Package required but not available: ‘rggobi’

Depends: includes the non-default packages:
  'RGtk2', 'gWidgetsRGtk2', 'cairoDevice', 'lattice', 'rggobi',
  'ggplot2', 'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PlasmaMutationDetector.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘S4Vectors’
No protocol specified

(R:31762): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:31770): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:31778): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:31786): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:31812): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:31840): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
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:31848): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:31856): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:31864): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:31878): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
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 10.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.7Mb
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/3.6/plot3Drgl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
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 138-146 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Failed to open file /Users/urbanek/Library/Caches/R/rerddap/d3691d4726dcf37b41ff22352dc3ac7e.nc.
--- failed re-building ‘using_plotdap.Rmd’

SUMMARY: processing the following file failed:
  ‘using_plotdap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘pmc_tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: subplex

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘OpenCPU.Rmd’ using rmarkdown
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.
--- finished re-building ‘OpenCPU.Rmd’

--- re-building ‘vignette.Rmd’ using rmarkdown
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.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    R      6.8Mb
    data   4.0Mb
No protocol specified
Namespace in Imports field not imported from: ‘combinat’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
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 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

SUMMARY: processing the following file failed:
  ‘polynomials.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘VariantAnnotation’
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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/3.6/PPQplan.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
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.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
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.
No protocol specified
Warning in normalizePath(f2) :
  path[1]="webshot83bd39d2f15.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot83bd39d2f15.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PPQplan-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘PerfMeas’
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/3.6/predict3d.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
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: predict3d
No protocol specified
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
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/3.6/prim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gurobi', 'Rsymphony'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
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 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘jtools’ ‘modelr’ ‘prediction’ ‘rlang’ ‘tidyr’
  All declared Imports should be used.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.9Mb
Package suggested but not available for checking: ‘EBImage’
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘proftools.Rnw’ using knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
--- failed re-building ‘proftools.Rnw’

SUMMARY: processing the following file failed:
  ‘proftools.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'qtbase', 'RGtk2', 'cairoDevice', 'gWidgetsRGtk2'
Running ‘testthat.R’ [64s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 279 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 10 ]
  1.  Error: cross_validation (@test_diagnostics.R#20) 
  2.  Error: cross_validation_logistic (@test_diagnostics.R#46) 
  3.  Error: cross_validation_extra_regressors (@test_diagnostics.R#66) 
  4.  Error: cross_validation_default_value_check (@test_diagnostics.R#81) 
  5.  Error: performance_metrics (@test_diagnostics.R#91) 
  6.  Error: fit_predict_no_changepoints (@test_prophet.R#28) 
  7.  Error: fit_predict_changepoint_not_in_history (@test_prophet.R#42) 
  8.  Error: auto_weekly_seasonality (@test_prophet.R#415) 
  9.  Error: (unknown) (@test_stan_functions.R#4) 
  10. Error: (unknown) (@test_stan_functions.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'org.Hs.eg.db'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.0Mb
Package suggested but not available for checking: ‘zoo’
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ptinpoly.Rcheck/00install.out’ for details.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pulseTD.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Data_Model.Rmd’ using rmarkdown
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.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
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.
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
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.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
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 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PWFSLSmoke.Rmd’

SUMMARY: processing the following file failed:
  ‘PWFSLSmoke.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
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/3.6/qpcR.Rcheck/00install.out’ for details.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Found the following executable file:
  src/LICENSES/LZ4_LICENSE.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qtbase.Rcheck/00install.out’ for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
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/3.6/qtlc.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs  11.2Mb
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/3.6/QuantifQuantile.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.9Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/R2GUESS.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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/3.6/R330.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
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
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]="webshot11ecc22868ec0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot11ecc22868ec0.png': No such file or directory
Quitting from lines 285-287 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RAbHIT-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RAbHIT-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.1Mb
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Matrix’ ‘PharmacoGx’ ‘cluster’
  All declared Imports should be used.
No protocol specified
  No protocol specified
  Note: found 26 marked UTF-8 strings
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/3.6/RadOnc.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
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/3.6/RAINBOWR.Rcheck/00install.out’ for details.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAPIDR.Rcheck/00install.out’ for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   9.6Mb
Package suggested but not available for checking: ‘rpanel’
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/3.6/rase.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
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: Rcpp

Attaching package: 'lubridate'

The following objects are masked from 'package:data.table':

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

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

    date

Loading required package: ggplot2

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

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
No protocol specified

(R:15712): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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/3.6/rayshader.Rcheck/00install.out’ for details.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  31.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rblpapi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RCAL-vig.Rnw’ using Sweave
Loading required package: trust

Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.BiclustGUI.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/3.6/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.TeachingDemos.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rcplex.Rcheck/00install.out’ for details.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    libs      1.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppClassic.Rcheck/00install.out’ for details.
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      25.5Mb
    libs      9.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.2Mb
    libs      4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rcrypt.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
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 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rdf_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rdf_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rdist.Rcheck/00install.out’ for details.
Running examples in ‘Rdsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readsync
> ### Title: Syncing file-backed variables.
> ### Aliases: readsync writesync
> 
> ### ** Examples
> 
> library(parallel)
> c2 <- makeCluster(2)
> mgrinit(c2)
Warning in for (v in val) { :
  closing unused connection 6 (<-localhost:11715)
Warning in for (v in val) { :
  closing unused connection 5 (<-localhost:11715)
[[1]]
[1] 0

[[2]]
[1] 0

> mgrmakevar(c2,"x",1,1,fs=TRUE)
Error in bigmemory::filebacked.big.matrix(nrow = nr, ncol = nc, type = vartype,  : 
  Backing file already exists! Either remove or specify
           different backing file
Calls: mgrmakevar -> <Anonymous>
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
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 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.1Mb
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/3.6/red.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.7Mb
Packages suggested but not available for checking: 'interval', 'Icens'
Package unavailable to check Rd xrefs: ‘interval’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
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: 'rENA'

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

    show

Loading required package: ggplot2

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

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
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: '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


Attaching package: 'rENA'

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

    show

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/resemble.Rcheck/00install.out’ for details.
sh: system_profiler: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: system_profiler: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: system_profiler: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: system_profiler: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: system_profiler: command not found
sh: system_profiler: command not found
sh: system_profiler: command not found
sh: system_profiler: command not found
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.
Package suggested but not available for checking: ‘rsolr’
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/3.6/restlos.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [8s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 3. Error: Properties are automatically converted in inherited classes (@test-
  Typea new-style class can't have only classic bases
  Backtrace:
   1. reticulate::PyClass(...)
   2. bt$type(classname, inherit, do.call(reticulate::dict, defs))
   3. reticulate:::py_call_impl(callable, dots$args, dots$keywords)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 114 | SKIPPED: 42 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: Can inherit from a Python class (@test-python-class.R#57) 
  2. Error: Can inherit from multiple Python classes (@test-python-class.R#84) 
  3. Error: Properties are automatically converted in inherited classes (@test-python-class.R#166) 
  
  Error: testthat unit tests failed
  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/3.6/retistruct.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘RTriangle’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘log_parsing.Rmd’ using rmarkdown
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.
Read 1000 items
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
--- finished re-building ‘log_parsing.Rmd’

--- re-building ‘url_parsing.Rmd’ using rmarkdown
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 'url_parsing.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘url_parsing.Rmd’

SUMMARY: processing the following file failed:
  ‘url_parsing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package suggested but not available for checking: ‘MKmisc’
Running examples in ‘RFLPtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFLPtools-package
> ### Title: Tools to analyse RFLP-data
> ### Aliases: RFLPtools-package RFLPtools
> ### Keywords: package multivariate cluster
> 
> ### ** Examples
> 
> data(RFLPdata)
> res <- RFLPdist(RFLPdata)
> plot(hclust(res[[1]]), main = "Euclidean distance")
> 
> par(mfrow = c(1,2))
> plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
> RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
> 
> data(RFLPref)
> RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
> 
> 
> library(MKmisc)
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Errors in running code in vignettes:
when running code in ‘RFLPtools.Rnw’
  ...
 - attr(*, "Diag")= logi FALSE
 - attr(*, "Upper")= logi FALSE
 - attr(*, "method")= chr "maximum"
 - attr(*, "call")= language dist(x = x, method = "maximum")

> library(MKmisc)

  When sourcing ‘RFLPtools.R’:
Error: there is no package called ‘MKmisc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFLPtools.Rnw’ using Sweave
Loading required package: RColorBrewer

Error: processing vignette 'RFLPtools.Rnw' failed with diagnostics:
 chunk 5 (label = cor) 
Error in library(MKmisc) : there is no package called ‘MKmisc’

--- failed re-building ‘RFLPtools.Rnw’

SUMMARY: processing the following file failed:
  ‘RFLPtools.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
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 object is masked from 'package:kableExtra':

    group_rows

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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
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 object is masked from 'package:kableExtra':

    group_rows

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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RGCxGC.Rcheck/00install.out’ for details.
installed size is 144.9Mb
  sub-directories of 1Mb or more:
    libs      142.0Mb
    pictures    1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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/3.6/rgl.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    4.2Mb
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

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.
Error(s) in re-building vignettes:
--- re-building ‘WebGL.Rmd’ using rmarkdown
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.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
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 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
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 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
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/3.6/rglwidget.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'graph', 'gWidgetsRGtk2', 'hyperdraw', 'hypergraph', 'playwith',
  'pmg', 'rggobi', 'Rgraphviz', 'SVGAnnotation'
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  11.1Mb
    libs   9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
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
--- failed re-building ‘intro_rhandsontable.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_rhandsontable.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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/3.6/RHRV.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
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.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RInside.Rcheck/00install.out’ for details.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.2Mb
Running examples in ‘RISmed-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cited
> ### Title: Number of citations
> ### Aliases: Cited
> 
> ### ** Examples
> 
> res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
> Cited(res)
Warning in readLines(the_url) :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Unknown Error'
Error in readLines(the_url) : 
  cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor'
Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
Execution halted
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
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/3.6/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.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Packages suggested but not available for checking:
  'Biobase', 'genefilter', 'golubEsets'
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/3.6/Rknots.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 44.4Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
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/3.6/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rLindo.Rcheck/00install.out’ for details.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Missing or unexported object: ‘tidyr::one_of’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
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/3.6/RMark.Rcheck/00install.out’ for details.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.7Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rmpi.Rcheck/00install.out’ for details.
Package required but not available: ‘splineTimeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Packages suggested but not available for checking: 'topGO', 'DESeq'
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doxygen   1.5Mb
    libs      3.2Mb
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.4Mb
Found the following executable files:
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R1/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R2/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R3/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R8/10/fid
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
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 188-195 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Column `is_oa` is unknown
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  17.0Mb
Package required but not available: ‘gprege’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RobLoxBioC.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
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/3.6/RockFab.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/3.6/ROCS.Rcheck/00install.out’ for details.
Package required but not available: ‘clpAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
sh: cmake: command not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
sh: cmake: command not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
sh: cmake: command not found
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.
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROracle.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/3.6/rotations.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    2.1Mb
    tests   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpanel.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/3.6/Rpdb.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpg.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
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.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
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
--- failed re-building ‘rpivotTableIntroduction.Rmd’

SUMMARY: processing the following file failed:
  ‘rpivotTableIntroduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
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/3.6/Rpolyhedra.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpoppler.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.2Mb
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/3.6/Rquake.Rcheck/00install.out’ for details.
installed size is 90.3Mb
  sub-directories of 1Mb or more:
    libs  89.7Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rrd.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/3.6/RRphylo.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘mvMORPH’
  All declared Imports should be used.
Error(s) in re-building vignettes:
--- re-building ‘rrtable.Rmd’ using rmarkdown
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)
--- failed re-building ‘rrtable.Rmd’

SUMMARY: processing the following file failed:
  ‘rrtable.Rmd’

Error: Vignette re-building failed.
Execution halted
No protocol specified

(R:70774): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70780): 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:70786): 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:70792): 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:70816): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70840): 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:70846): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70852): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70858): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:70870): 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 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rsconnect)
  > 
  > test_check("rsconnect")
  ── 1. Failure: linter warns about absolute paths and relative paths (@test-lint.
  as.numeric(absPathLintedIndices) not identical to 15.
  Lengths differ: 0 is not 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 257 | SKIPPED: 25 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: linter warns about absolute paths and relative paths (@test-lint.R#18) 
  
  Error: testthat unit tests failed
  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/3.6/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.
File ‘rsgcc/libs/rsgcc.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  25.5Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 46.4Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     1.2Mb
    libs  142.5Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
installed size is 233.2Mb
  sub-directories of 1Mb or more:
    libs  230.5Mb
installed size is 69.5Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
installed size is 61.3Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
Running ‘run_test.R’ [7s/7s]
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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.9Mb
    projects   2.7Mb
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RTransProb.Rcheck/00install.out’ for details.
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.8Mb
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 581 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 30 ]
  1. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  2. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  3. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  4. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  5. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  6. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  7. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  8. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  9. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.5Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
Running examples in ‘rviewgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: rViewGraph
> ### Title: This is a function to create and start the Java graph animation
> ###   GUI.
> ### Aliases: rViewGraph rViewGraph.default rViewGraph.Matrix
> ###   rViewGraph.igraph
> ### Keywords: graph
> 
> ### ** Examples
> 
> # 
> # Viewing an Erdos Renyui random graph specified by random edges.
> f = sample(100,size=200,replace=TRUE)
> t = sample(100,size=200,replace=TRUE)
> vft = rViewGraph(cbind(f,t))
Error in .jnew("rviewgraph/RViewGraph", v, f, t, x, y, directed, running) : 
  java.awt.HeadlessException
Calls: rViewGraph ... rViewGraph.default -> rViewGraphCore -> init -> .jnew
Execution halted
installed size is 62.9Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     58.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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/3.6/RWiener.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
No protocol specified
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Running examples in ‘sae2-Ex.R’ failed
The error most likely occurred in:

> ### Name: geo_ratios
> ### Title: Compute rates or ratios for a set of geographic entities over a
> ###   set of years
> ### Aliases: geo_ratios
> 
> ### ** Examples
> 
> require(survey)
> require(MASS)
> D <- 20 # number of domains
> T <- 5 # number of years
> samp <- 16 # number of sample cases per domain
> set.seed(1)
> # use conditional.mean=TRUE to generate true small area values
> # without sampling error
> Y.list <- mvrnormSeries(D=D, T=T, rho.dyn=.9, sigma.v.dyn=1, 
+    sigma.u.dyn=.19, sigma.e=diag(5), conditional.mean=TRUE)
> # generate sampling errors
> e <- rnorm(samp * T * D, mean=0, sd=4)
> Y <- Y.list[[2]] + tapply(e, rep(1:100, each=16), mean) 
> data <- data.frame(Y=Y, X=rep(1:T, times=D))
> # model fit with the true sampling variances
> result.dyn  <- eblupDyn(Y ~ X, D, T, vardir = diag(100), data=data)
Error in y - X %*% B_Est : non-conformable arrays
Calls: eblupDyn -> dynRYfit
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/3.6/SafeBayes.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.8Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.4Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'mixer', 'org.Sc.sgd.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
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
--- failed re-building ‘sass.Rmd’

SUMMARY: processing the following file failed:
  ‘sass.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
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.
--- finished re-building ‘gettingstarted.Rmd’

--- re-building ‘article.Rnw’ using knitr
Error: processing vignette 'article.Rnw' failed with diagnostics:
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!
--- failed re-building ‘article.Rnw’

SUMMARY: processing the following file failed:
  ‘article.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dynwrap’

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/3.6/scpm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘oligoClasses’
Packages required but not available: 'ALL', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘seasonalview’
Package unavailable to check Rd xrefs: ‘seasonalview’
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  13.5Mb
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/3.6/SEERaBomb.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
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/3.6/Segmentor3IsBack.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running examples in ‘SemNetCleaner-Ex.R’ failed
The error most likely occurred in:

> ### Name: bin2resp
> ### Title: Binary Responses to Character Responses
> ### Aliases: bin2resp
> 
> ### ** Examples
> 
> # Toy example
> raw <- open.animals[c(1:10),-c(1:3)]
> 
> # Clean and prepocess data
> clean <- textcleaner(raw, partBY = "row", dictionary = "animals")
IDs refer to row number
No protocol specified
No protocol specified
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: textcleaner ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SeqFeatR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘airway’
Error(s) in re-building vignettes:
  ...
--- re-building ‘different_thinners.Rmd’ using rmarkdown
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.
--- finished re-building ‘different_thinners.Rmd’

--- re-building ‘simulate_rnaseq.Rmd’ using rmarkdown
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'
--- failed re-building ‘simulate_rnaseq.Rmd’

SUMMARY: processing the following file failed:
  ‘simulate_rnaseq.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   8.7Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sequenza.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Packages suggested but not available for checking:
  'loomR', 'SingleCellExperiment', 'MAST', 'monocle'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 187.2Mb
  sub-directories of 1Mb or more:
    doc      12.0Mb
    libs    171.2Mb
    sqlite    1.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sf1.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
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
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
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.
--- finished re-building ‘sf6.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sgPLS.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘SGP.Rmd’ using rmarkdown
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
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
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_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
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_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
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/3.6/shapes.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.2Mb
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/3.6/shinyRGL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘edgeR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
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
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘maftools’

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

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/3.6/SimEUCartelLaw.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.9Mb
Package suggested but not available for checking: ‘topologyGSA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
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 252-258 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'topologyGSA'
--- failed re-building ‘simPATHy.Rmd’

SUMMARY: processing the following file failed:
  ‘simPATHy.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimRAD.Rcheck/00install.out’ for details.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  18.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  29.9Mb
Error(s) in re-building vignettes:
--- re-building ‘basics.Rmd’ using rmarkdown
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
--- failed re-building ‘basics.Rmd’

--- re-building ‘iframes.Rmd’ using rmarkdown
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 76-87 (iframes.Rmd) 
Error: processing vignette 'iframes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘iframes.Rmd’

--- re-building ‘pdfs.Rmd’ using rmarkdown
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 31-33 (pdfs.Rmd) 
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘pdfs.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
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 88-93 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
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.
--- finished re-building ‘shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘iframes.Rmd’ ‘pdfs.Rmd’ ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SmartSVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SMITIDstruct’
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/3.6/smoothAPC.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   8.9Mb
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.5Mb
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/3.6/snpReady.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.5Mb
plot.soo_function: no visible global function definition for
  ‘terrain.colors’
plot.soo_function: no visible binding for global variable ‘image’
plot.soo_function: no visible binding for global variable ‘contour’
plot3d: no visible global function definition for ‘persp3d’
plot3d: no visible global function definition for ‘terrain.colors’
random_parameters.soo_function: no visible global function definition
  for ‘runif’
random_rotation_matrix: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  contour image persp3d runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "contour", "image")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error(s) in re-building vignettes:
--- re-building ‘novel_solutions.Rmd’ using rmarkdown
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.
--- finished re-building ‘novel_solutions.Rmd’

--- re-building ‘shiny_apps.Rmd’ using rmarkdown
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.
--- finished re-building ‘shiny_apps.Rmd’

--- re-building ‘understanding_sortable_js.Rmd’ using rmarkdown
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]="webshot2dfb12c986ff.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot2dfb12c986ff.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
--- failed re-building ‘understanding_sortable_js.Rmd’

SUMMARY: processing the following file failed:
  ‘understanding_sortable_js.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'r2cytoscape', 'BiocStyle', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Package unavailable to check Rd xrefs: ‘ALL’
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    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, colnames, dirname, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, mapply, match, mget, order, paste, pmax,
    pmax.int, pmin, pmin.int, rank, rbind, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Identifing all possible orderings..
Total run time: 1.46 secs
Identifing all possible orderings..
Total run time: 0.79 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]="webshot1036025ae8906.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1036025ae8906.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
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Missing or unexported objects:
  ‘pomp::covariate_table’ ‘pomp::gillespie_hl’
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  31.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
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]="webshot4c28b900111.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4c28b900111.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
--- failed re-building ‘intro_sparkline.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_sparkline.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
Running examples in ‘spatialEco-Ex.R’ failed
The error most likely occurred in:

> ### Name: hli
> ### Title: Heat Load Index
> ### Aliases: hli
> 
> ### ** Examples
> 
>   library(raster)
Loading required package: sp

Attaching package: ‘raster’

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

    shift

>   data(elev)
>   heat.load <- hli(elev)

 *** caught segfault ***
address 0x113af6ff8, 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(x, opt = "slope", unit = "degrees")
 4: raster::terrain(x, opt = "slope", unit = "degrees")
 5: hli(elev)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.0Mb
No protocol specified
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    R      5.3Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.8Mb
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/3.6/spatsurv.Rcheck/00install.out’ for details.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   9.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.2Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
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/3.6/sphereplot.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/3.6/SphericalCubature.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/3.6/sppmix.Rcheck/00install.out’ for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.0Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 57.7Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
No protocol specified

(R:89340): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:89350): 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:89361): 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:89371): 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:89399): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:89431): 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:89441): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:89451): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:89461): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:89477): 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:89493): 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/7s]
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 ...
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    include  10.2Mb
    lib       1.9Mb
Package which this enhances but not available for checking: ‘mnlogit’
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
No protocol specified

(R:4520): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4528): 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:4536): 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:4544): 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:4570): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4598): 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:4606): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4614): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4622): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:4636): 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.
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/3.6/StatDA.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   4.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

> ### Name: maxchi
> ### Title: Stepwise detection of recombination breakpoints using MaxChi
> ### Aliases: maxchi
> ### Keywords: htest
> 
> ### ** Examples
>  demo(maxchi) 


	demo(maxchi)
	---- ~~~~~~

> inputFile<- system.file("extdata", "simulinfile.txt", package = "stepwise")

> breaks<-c(531,616,810)

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘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.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages suggested but not available for checking: 'limma', 'samr'
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/3.6/stream.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  10.0Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/STRMPS.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/3.6/stR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
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 13-17 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
there is no package called 'seasonal'
--- failed re-building ‘stRvignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stRvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Package required but not available: ‘EmiStatR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Namespaces in Imports field not imported from:
  ‘UpSetR’ ‘alluvial’ ‘geoR’ ‘gridBase’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SubVis.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
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
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
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/3.6/supervisedPRIM.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/3.6/suropt.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/3.6/Surrogate.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/survHE.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Package unavailable to check Rd xrefs: ‘survJamda’
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs   5.3Mb
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
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/3.6/symbolicDA.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘HTML.Rmd’ using rmarkdown
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
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
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

--- finished re-building ‘tables.Rnw’

SUMMARY: processing the following file failed:
  ‘HTML.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.1Mb
Packages suggested but not available for checking:
  'limma', 'edgeR', 'DESeq2', 'S4Vectors'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.7Mb
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.9Mb
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
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/3.6/tensorsparse.Rcheck/00install.out’ for details.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Packages suggested but not available for checking: 'Rsymphony', 'gurobi'
Error(s) in re-building vignettes:
--- re-building ‘classes.Rmd’ using rmarkdown
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.
--- finished re-building ‘classes.Rmd’

--- re-building ‘kable.Rmd’ using rmarkdown
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.
--- finished re-building ‘kable.Rmd’

--- re-building ‘rmarkdown.Rmd’ using rmarkdown
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.
--- finished re-building ‘rmarkdown.Rmd’

--- re-building ‘slickr.Rmd’ using rmarkdown
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
--- failed re-building ‘slickr.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
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.
--- finished re-building ‘tests_and_coverage.Rmd’

--- re-building ‘tex_packages.Rmd’ using rmarkdown
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.
--- finished re-building ‘tex_packages.Rmd’

--- re-building ‘tikz.Rmd’ using rmarkdown
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.
--- finished re-building ‘tikz.Rmd’

SUMMARY: processing the following file failed:
  ‘slickr.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/text2vec.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tidyxl.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
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
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/7s]
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 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: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkrgl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkRplotR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tmod.rmd’ using rmarkdown
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 51-59 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
there is no package called 'limma'
--- failed re-building ‘tmod.rmd’

SUMMARY: processing the following file failed:
  ‘tmod.rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rpoppler’
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/3.6/tolerance.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RGtk2', 'gWidgetsRGtk2'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/topologyGSA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ToxicoGx.Rcheck/00install.out’ for details.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
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
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
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

Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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/3.6/TreeLS.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs      9.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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/3.6/treespace.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is 85.2Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  80.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
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
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building failed.
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/3.6/trinROC.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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/3.6/TSclust.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
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/3.6/TSCS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
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 16, 2019 10:07:08 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 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  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
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
Error(s) in re-building vignettes:
--- re-building ‘TSplotly.Rmd’ using rmarkdown
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: TSplotly
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Loading required package: plotly

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]="webshota8915d600bdd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshota8915d600bdd.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
--- failed re-building ‘TSplotly.Rmd’

SUMMARY: processing the following file failed:
  ‘TSplotly.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Plotting_Time_Series.Rmd’ using rmarkdown
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]="webshot100af396368a2.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot100af396368a2.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
--- failed re-building ‘Plotting_Time_Series.Rmd’

SUMMARY: processing the following file failed:
  ‘Plotting_Time_Series.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TTAinterfaceTrendAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ttScreening.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/3.6/TukeyRegion.Rcheck/00install.out’ for details.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following executable files:
  inst/examples/ko.txt
  inst/examples/ru/koi8-r.txt
  src/uchardet/test/ru/koi8-r.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
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
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
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/3.6/ungroup.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   6.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  21.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 144.7Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     143.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown
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]="webshotcf6e309706a3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotcf6e309706a3.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
--- failed re-building ‘basic_usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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/3.6/VecStatGraphs3D.Rcheck/00install.out’ for details.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
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/3.6/vegan3d.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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/3.6/vennplot.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Package required but not available: ‘coRdon’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘sp’ ‘viridis’
  All declared Imports should be used.
installed size is 55.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  54.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/viromeBrowser.Rcheck/00install.out’ for details.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VSE.Rcheck/00install.out’ for details.
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    libs  66.1Mb
Running examples in ‘walker-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_predict
> ### Title: Prediction intervals for walker object
> ### Aliases: plot_predict
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 60
> slope <- 0.0001 + cumsum(rnorm(n, 0, sd = 0.01))
> beta <- numeric(n)
> beta[1] <- 1
> for(i in 2:n) beta[i] <- beta[i-1] + slope[i-1]
> ts.plot(beta)                
> x <- rnorm(n, 1, 0.5)
> alpha <- 2
> ts.plot(beta * x)
> 
> signal <- alpha + beta * x
> y <- rnorm(n, signal, 0.25)
> ts.plot(cbind(signal, y), col = 1:2)
> data_old <- data.frame(y = y[1:(n-10)], x = x[1:(n-10)])
> rw2_fit <- walker(y ~ 1 + 
+                     rw2(~ -1 + x,
+                         beta_prior = c(0, 10), 
+                         sigma_prior = c(0, 10), 
+                         slope_prior = c(0, 10)), 
+                   sigma_y_prior = c(0, 10), 
+                   beta_prior = c(0, 10),
+                   iter = 400, chains = 1, data = data_old)

SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.000936 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 9.36 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 400 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
> 
> pred <- predict(rw2_fit, newdata = data.frame(x=x[(n-9):n]))
Stan model 'walker_lm' does not contain samples.
Stan model 'walker_lm' does not contain samples.
Error in matrix(0, n_iter, 0) : non-numeric matrix extent
Calls: predict -> predict.walker_fit -> matrix
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘walker.Rmd’ using rmarkdown
Warning in engine$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 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘walker.Rmd’

SUMMARY: processing the following file failed:
  ‘walker.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘bioacoustics’
Package unavailable to check Rd xrefs: ‘bioacoustics’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
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/3.6/WhopGenome.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
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
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: '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]="webshot13f204f5efc8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13f204f5efc8.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
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
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/3.6/x3ptools.Rcheck/00install.out’ for details.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/XGR.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.8Mb
Package suggested but not available for checking: ‘ggtree’
Error(s) in re-building vignettes:
  ...
--- re-building ‘gammaproteobacteria.Rmd’ using rmarkdown
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:
there is no package called 'ggtree'
--- failed re-building ‘gammaproteobacteria.Rmd’

SUMMARY: processing the following file failed:
  ‘gammaproteobacteria.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 35.8Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/YuGene.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/zenplots.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(s) in re-building vignettes:
--- re-building ‘heatmapTable.Rmd’ using rmarkdown
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
--- finished re-building ‘heatmapTable.Rmd’

--- re-building ‘ztable.Rmd’ using rmarkdown
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.
--- finished re-building ‘ztable.Rmd’

--- re-building ‘ztable_update.Rmd’ using rmarkdown
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)
--- failed re-building ‘ztable_update.Rmd’

SUMMARY: processing the following file failed:
  ‘ztable_update.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AbsFilterGSEA.Rcheck/00install.out' for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
record: no visible global function definition for 'str2lang'
Undefined global functions or variables:
  str2lang
Found the following significant warnings:
  Note: possible error in 'set.seed(100, sample.kind = "Rejection")': unused argument (sample.kind = "Rejection") 
See 'd:/Rcompile/CRANpkg/local/3.5/assignR.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
QA: possible error in set.seed(100, sample.kind = "Rejection"): unused
  argument (sample.kind = "Rejection")
Missing or unexported object: 'grDevices::hcl.colors'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   1.8Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'baseline.lowpass.R' line 4
  Warning: unable to re-encode 'baseline.medianWindow.R' line 3
  Warning: unable to re-encode 'baseline.modpolyfit.R' line 4
See 'd:/Rcompile/CRANpkg/local/3.5/baseline.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.2Mb
Packages suggested but not available for checking: 'bcmapsdata' 'doMC'
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("blockRAR")
  Loading required package: blockRAR
  -- 1. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#10) 
  ...$NULL not equal to 1.
  1/1 mismatches
  [1] 0.8 - 1 == -0.2
  
  -- 2. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#23) 
  ...$NULL not equal to 0.
  1/1 mismatches
  [1] 0.1 - 0 == 0.1
  
  == testthat results  ===========================================================
  [ OK: 50 | SKIPPED: 0 | WARNINGS: 1021 | FAILED: 2 ]
  1. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#10) 
  2. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
clusterplots: no visible global function definition for 'par'
clusterplots: no visible global function definition for 'rainbow'
clusterplots: no visible global function definition for 'plot'
clusterplots: no visible global function definition for 'axis'
clusterplots: no visible global function definition for 'lines'
diagplots: no visible global function definition for 'par'
diagplots: no visible global function definition for 'plot'
diagplots: no visible global function definition for 'hist'
tseriesca: no visible global function definition for 'rgamma'
tseriesca: no visible global function definition for 'runif'
tseriesca: no visible global function definition for 'dbeta'
tseriesca: no visible global function definition for 'dgamma'
tseriescm: no visible global function definition for 'rgamma'
tseriescm: no visible global function definition for 'runif'
tseriescm: no visible global function definition for 'dbeta'
tseriescm: no visible global function definition for 'dgamma'
tseriescq: no visible global function definition for 'rgamma'
tseriescq: no visible global function definition for 'runif'
tseriescq: no visible global function definition for 'dbeta'
tseriescq: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
Running examples in 'bnspatial-Ex.R' failed
The error most likely occurred in:

> ### Name: bnspatial
> ### Title: Spatialize the Bayesian network
> ### Aliases: bnspatial
> 
> ### ** Examples
> 
> list2env(ConwyData, environment())
<environment: R_GlobalEnv>
> 
> network <- LandUseChange
> spatialData <- c(ConwyLU, ConwySlope, ConwyStatus)
> lookup <- LUclasses
> 
> bn <- bnspatial(network, 'FinalLULC', spatialData, lookup)

"CurrentLULC" points to:
 ->  ConwyLU 

With states:
forest    arable    other

Represented by integer values:
2 <-> 3 <-> 1
----------------------------------

"Slope" points to:
 ->  ConwySlope 

With states:
flat    moderate    steep

Discretized by intervals:
-Inf <-> 1 <-> 7 <-> Inf
----------------------------------

"LegalStatus" points to:
 ->  ConwyStatus 

With states:
public    private    protected

Represented by integer values:
4 <-> 3 <-> 1
----------------------------------
Error in NextMethod("compile") : no method to invoke
Calls: bnspatial ... querygrain.grain -> compile -> compile.grain -> NextMethod
Execution halted
Error in re-building vignettes:
  ...
Loading required package: raster
Loading required package: sp
Quitting from lines 93-114 (bnspatial.Rmd) 
Error: processing vignette 'bnspatial.Rmd' failed with diagnostics:
no method to invoke
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.6Mb
Error in re-building vignettes:
  ...
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: D:/temp/RtmpmWyItW/RLIBS_2986c405f7a40/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: D:/temp/RtmpmWyItW/RLIBS_2986c405f7a40/rgdal/proj
 Linking to sp version: 1.3-2 
This is secr 4.1.0. For overview type ?secr

Attaching package: 'secr'

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

    flip, rotate, shift, trim

Quitting from lines 278-279 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
could not find function "hcl.colors"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/cellWise.Rcheck/00install.out' for details.
Packages required but not available: 'MomTrunc' 'tlrmvnmvt'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Note: possible error in 'trimws(x, which = "both", ': unused argument (whitespace = "[ \t\r\n]") 
See 'd:/Rcompile/CRANpkg/local/3.5/clean.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
clean_character: possible error in trimws(x, which = "both", whitespace
  = "[ \t\r\n]"): unused argument (whitespace = "[ \t\r\n]")
Running examples in 'clean-Ex.R' failed
The error most likely occurred in:

> ### Name: clean
> ### Title: Clean column data to a class
> ### Aliases: clean clean.data.frame clean_logical clean_factor
> ###   clean_numeric clean_character clean_currency clean_Date clean_POSIXct
> 
> ### ** Examples
> 
> clean_logical(c("Yes", "No"))   # English
[1]  TRUE FALSE
> clean_logical(c("Oui", "Non"))  # French
[1]  TRUE FALSE
> clean_logical(c("ya", "tidak")) # Indonesian
[1]  TRUE FALSE
> clean_logical(x = c("Positive", "Negative", "Unknown", "Some value"),
+               true = "pos", false = "neg")
[1]  TRUE FALSE    NA    NA
> 
> gender_age <- c("male 0-50", "male 50+", "female 0-50", "female 50+")
> clean_factor(gender_age, c("M", "F"))
[1] M M F F
Levels: M F
> clean_factor(gender_age, c("Male", "Female"))
[1] Male   Male   Female Female
Levels: Male Female
> clean_factor(gender_age, c("0-50", "50+"), ordered = TRUE)
[1] 0-50 50+  0-50 50+ 
Levels: 0-50 < 50+
> 
> clean_Date("13jul18", "ddmmmyy")
[1] "2018-07-13"
> clean_Date("12 august 2010")
Cleaning dates using format 'dd mmmm yyyy' ('%d %B %Y')
[1] "2010-08-12"
> clean_Date("12 06 2012")
Cleaning dates using format 'dd mm yyyy' ('%d %m %Y')
[1] "2012-06-12"
> clean_Date(36526) # Excel date
Cleaning dates using Excel format
[1] "2000-01-01"
> clean_Date("43658")
Cleaning dates using Excel format
[1] "2019-07-12"
> clean_Date("14526", "Excel") # "1939-10-08"
[1] "1939-10-08"
> 
> clean_POSIXct("Created log on 2019/04/11 11:23 by user Joe")
[1] "2019-04-11 11:23:00 CEST"
> 
> clean_numeric("qwerty123456")
[1] 123456
> clean_numeric("Positive (0.143)")
[1] 0.143
> clean_numeric("0,143")
[1] 0.143
> 
> clean_character("qwerty123456")
Error in trimws(x, which = "both", whitespace = "[ \t\r\n]") : 
  unused argument (whitespace = "[ \t\r\n]")
Calls: clean_character
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 48-58 (climbeR_examples.Rmd) 
Error: processing vignette 'climbeR_examples.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'indecis_indices.R' lines 4067, 4098
See 'd:/Rcompile/CRANpkg/local/3.5/ClimInd.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ClussCluster.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ClusterR.Rcheck/00install.out' for details.
Problems with news in 'inst/NEWS.Rd':
  inst/NEWS.Rd:833: unknown macro '\proglang'
  inst/NEWS.Rd:893: unknown macro '\proglang'
  inst/NEWS.Rd:1034: unknown macro '\proglang'
  inst/NEWS.Rd:1050: unknown macro '\proglang'
  inst/NEWS.Rd:1052: unknown macro '\proglang'
  inst/NEWS.Rd:1057: unknown macro '\proglang'
Error in re-building vignettes:
  ...
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Execution halted
is_deprecated: no visible global function definition for
  'warningCondition'
Undefined global functions or variables:
  warningCondition
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/CoSMoS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/cowplot.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Quitting from lines 70-73 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
no applicable method for 'depth' applied to an object of class "NULL"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/cplm.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.6Mb
Package suggested but not available for checking: 'tidyrules'
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 12-20 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
there is no package called 'tidyrules'
Execution halted
Packages required and available but unsuitable versions:
  'graphics' 'grDevices' 'stats' 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [265s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dabestr)
  Loading required package: boot
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("dabestr")
  -- 1. Failure: Using `grp` as x column is kosher (@test-unquoting.R#50)  -------
  df_analysed.result$control_size not equal to 54.
  1/1 mismatches
  [1] 40 - 54 == -14
  
  -- 2. Failure: Using `grp` as x column is kosher (@test-unquoting.R#51)  -------
  df_analysed.result$test_size not equal to 46.
  1/1 mismatches
  [1] 60 - 46 == 14
  
  -- 3. Failure: Using `grp` as x column is kosher (@test-unquoting.R#53)  -------
  df_analysed.result$difference not equal to -0.02769726.
  1/1 mismatches
  [1] 0.0367 - -0.0277 == 0.0644
  
  -- 4. Failure: Using `grp` as x column is kosher (@test-unquoting.R#54)  -------
  round(df_analysed.result$bca_ci_low, digits = 4) not equal to -0.1253.
  1/1 mismatches
  [1] -0.0725 - -0.125 == 0.0528
  
  -- 5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55)  -------
  df_analysed.result$bca_ci_high not equal to 0.07162217.
  1/1 mismatches
  [1] 0.146 - 0.0716 == 0.0742
  
  == testthat results  ===========================================================
  [ OK: 17 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 5 ]
  1. Failure: Using `grp` as x column is kosher (@test-unquoting.R#50) 
  2. Failure: Using `grp` as x column is kosher (@test-unquoting.R#51) 
  3. Failure: Using `grp` as x column is kosher (@test-unquoting.R#53) 
  4. Failure: Using `grp` as x column is kosher (@test-unquoting.R#54) 
  5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DALEX.Rcheck/00install.out' for details.
Running examples in 'DALEXtra-Ex.R' failed
The error most likely occurred in:

> ### Name: explain_scikitlearn
> ### Title: Wrapper for Python Scikit-Learn Models
> ### Aliases: explain_scikitlearn
> 
> ### ** Examples
> 
> library("DALEXtra")
> if(DALEXtra:::is_conda()) {
+    # Explainer build (Keep in mind that 18th column is target)
+    titanic_test <- read.csv(system.file("extdata", "titanic_test.csv", package = "DALEXtra"))
+    # Keep in mind that when pickle is being built and loaded,
+    # not only Python version but libraries versions has to match aswell
+    explainer <- explain_scikitlearn(system.file("extdata", "scikitlearn.pkl", package = "DALEXtra"),
+    yml = system.file("extdata", "testing_environment.yml", package = "DALEXtra"),
+    data = titanic_test[,1:17], y = titanic_test$survived)
+    plot(model_performance(explainer))
+ 
+    # Predictions with newdata
+    predict(explainer, titanic_test[1:10,1:17])
+ 
+ } else {
+   print('Conda is required.')
+ }
There already exists environment named the same as it is specified in .yml file - myenv. It will be used
Warning in system2(command = python, args = paste0("\"", config_script,  :
  running command '"C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe" "D:/temp/Rtmp4SELlH/RLIBS_2c6007aa716b2/reticulate/config/config.py"' had status 2
Warning: Error in python_config(python_version, required_module, python_version, : Error 2 occurred running C:/Users/CRAN/AppData/Local/r-miniconda/envs/myenv/python.exe 

Error: Yours environment has to match environment where pickle file was created. It also includes encoding, python version, and libraries version. Specifying .yml file or path to virtual environment may help. For more information look warnings() and then ?explain_scikitlearn
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DataVisualizations.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: unable to re-encode 'missing_value_impute.R' line 216
See 'd:/Rcompile/CRANpkg/local/3.5/DDPNA.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DepthProc.Rcheck/00install.out' for details.
ToXL.array: no visible global function definition for 'asplit'
Undefined global functions or variables:
  asplit
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DGM.Rcheck/00install.out' for details.
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc           9.7Mb
    htmlwidgets   5.9Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  Warning: unable to re-encode 'pnbeta.R' lines 12, 35
  Warning: unable to re-encode 'pnchisq.R' lines 263, 264, 265, 266, 648, 652, 654, 667, 675, 676, 716
  Warning: unable to re-encode 'qnchisq.R' lines 135, 136, 146, 147, 148, 149, 243, 248, 250
See 'd:/Rcompile/CRANpkg/local/3.5/DPQ.Rcheck/00install.out' for details.
Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dynwrap)
  > 
  > test_check("dynwrap")
  -- 1. Failure: Testing add_timings (@test-wrap_add_timings.R#43)  --------------
  all(abs(diffs - c(1, 0.5, 0.25)) < 0.1) isn't true.
  
  == testthat results  ===========================================================
  [ OK: 1256 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Testing add_timings (@test-wrap_add_timings.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'Ecfun-Ex.R' failed
The error most likely occurred in:

> ### Name: read.testURLs
> ### Title: Read a file produced by testURLs
> ### Aliases: read.testURLs
> ### Keywords: IO
> 
> ### ** Examples
> 
> # Test only 2 web sites, not the default 4,
> # and test only twice, not the default 10 times:
> tst <- testURLs(c(
+  PVI="http://en.wikipedia.org/wiki/Cook_Partisan_Voting_Index",
+  house="http://house.gov/representatives"),
+     n=2, maxFail=2)
1 
1580063355, PVI, FALSE 21.44 
1580063377, PVI, FALSE 21.21 
1580063398, house, TRUE 0.36 
2 
1580063398, PVI, FALSE 21.22 
1580063419, PVI, FALSE 21.2 
1580063441, house, TRUE 0.29 
> 
> # The above should have created a file 'testURLresults.csv'
> # in the working directory.  Read it.
> 
> dat <- read.testURLs()
Error in read.table(file = file, header = header, sep = sep, quote = quote,  : 
  more columns than column names
Calls: read.testURLs -> read.csv -> read.table
Execution halted
Running examples in 'EcoHydRology-Ex.R' failed
The error most likely occurred in:

> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
Running 'testthat.R' [16s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ECoL)
  > 
  > test_check("ECoL")
  -- 1. Failure: multiclass.result (@test_linearity.R#13)  -----------------------
  as.numeric(aux$L3) not equal to 0.01.
  1/1 mismatches
  [1] 0.00667 - 0.01 == -0.00333
  
  -- 2. Failure: multiclass.result (@test_neighborhood.R#16)  --------------------
  as.numeric(aux$N4) not equal to 0.00666667.
  1/1 mismatches
  [1] 0.0133 - 0.00667 == 0.00667
  
  == testthat results  ===========================================================
  [ OK: 97 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: multiclass.result (@test_linearity.R#13) 
  2. Failure: multiclass.result (@test_neighborhood.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/egg.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: 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

Quitting from lines 93-95 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(emba)
  > 
  > test_check("emba")
  -- 1. Failure: it returns correct results (@test-analysis.R#8)  ----------------
  count_models_that_predict_synergies(...) not equal to 25.
  1/1 mismatches
  [1] 26 - 25 == 1
  
  -- 2. Failure: it returns correct results (@test-analysis.R#10)  ---------------
  count_models_that_predict_synergies(...) not equal to 360.
  1/1 mismatches
  [1] 310 - 360 == -50
  
  -- 3. Failure: it returns correct results (@test-analysis.R#11)  ---------------
  count_models_that_predict_synergies(...) not equal to 312.
  1/1 mismatches
  [1] 334 - 312 == 22
  
  -- 4. Failure: it returns correct results (@test-analysis.R#12)  ---------------
  count_models_that_predict_synergies(...) not equal to 329.
  1/1 mismatches
  [1] 313 - 329 == -16
  
  -- 5. Failure: it returns correct results (@test-analysis.R#14)  ---------------
  count_models_that_predict_synergies(...) not equal to 119.
  1/1 mismatches
  [1] 91 - 119 == -28
  
  -- 6. Failure: it returns correct results (@test-analysis.R#15)  ---------------
  count_models_that_predict_synergies(...) not equal to 119.
  1/1 mismatches
  [1] 91 - 119 == -28
  
  == testthat results  ===========================================================
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
  1. Failure: it returns correct results (@test-analysis.R#8) 
  2. Failure: it returns correct results (@test-analysis.R#10) 
  3. Failure: it returns correct results (@test-analysis.R#11) 
  4. Failure: it returns correct results (@test-analysis.R#12) 
  5. Failure: it returns correct results (@test-analysis.R#14) 
  6. Failure: it returns correct results (@test-analysis.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/EMMIXgene.Rcheck/00install.out' for details.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(eurostat)
  > 
  > test_check("eurostat")
  -- 1. Failure: Countrycodes are labelled for factors (@test-all.R#93)  ---------
  levels(...) not equal to c("Finland", "Germany", "EU28").
  target is NULL, current is character
  
  -- 2. Failure: Countrycodes return NA for countrycode_nomatch = NA (@test-all.R#
  suppressWarnings(...) not equal to c("Finland", "Germany", NA).
  target is NULL, current is character
  
  -- 3. Failure: Countrycodes use eurostat for missing (@test-all.R#105)  --------
  suppressWarnings(...) not equal to c("Finland", "Germany", "European Union - 28 countries").
  target is NULL, current is character
  
  -- 4. Failure: custom_dic works (@test-all.R#111)  -----------------------------
  label_eurostat(c("FI", "DE"), dic = "geo", custom_dic = c(DE = "Germany")) not equal to c("Finland", "Germany").
  target is NULL, current is character
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 20 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: Countrycodes are labelled for factors (@test-all.R#93) 
  2. Failure: Countrycodes return NA for countrycode_nomatch = NA (@test-all.R#99) 
  3. Failure: Countrycodes use eurostat for missing (@test-all.R#105) 
  4. Failure: custom_dic works (@test-all.R#111) 
  
  Error: testthat unit tests failed
  Execution halted
Undocumented code objects:
  'caption.etable' 'caption<-.etable'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("fabletools")
  Loading required package: fabletools
  Error: A model specification is trained to a dataset using the `model()` function.
  Refer to the documentation in ?model for more details.
  Backtrace:
       x
    1. \-testthat::test_check("fabletools")
    2.   \-testthat:::test_package_dir(...)
    3.     \-testthat::test_dir(...)
    4.       \-testthat::source_test_setup(path, env)
    5.         \-testthat::source_dir(path, "^setup.*\\.[rR]$", env = env, wrap = FALSE)
    6.           \-base::lapply(files, source_file, env = env, chdir = chdir, wrap = wrap)
    7.             \-testthat:::FUN(X[[i]], ...)
    8.               \-base::eval(exprs, env)
    9.                 \-base::eval(exprs, env)
   10.                   \-us_deaths %>% feasts::STL(value) d:\RCompile\CRANpkg\local\3.5\fabletools.Rcheck\tests\testthat\setup-data.R:30:0
   11.                     +-base::withVisible(eval(quote(`_fseq`(`_lhs`)), env, env))
   12.                     \-base::eval(quote(`_fseq`(`_lhs`)), env, env)
   13.                       \-base::eval(quote(`_fseq`(`_lhs`)),
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
Found the following significant warnings:
  Note: possible error in 'set.seed(42, sample.kind = "Rounding")': unused argument (sample.kind = "Rounding") 
See 'd:/Rcompile/CRANpkg/local/3.5/fingertipscharts.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
create_test_data: possible error in set.seed(42, sample.kind =
  "Rounding"): unused argument (sample.kind = "Rounding")
Error in re-building vignettes:
  ...
Quitting from lines 140-156 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
Faceting variables must have at least one value
Execution halted
Depends: includes the non-default packages:
  'gWidgets' 'tcltk' 'tkrplot' 'RGtk2' 'gWidgetsRGtk2' 'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking: 'doMC' 'RSvgDevice'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   1.8Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Found the following significant warnings:
  Warning: unable to re-encode 'isoweek.R' line 40
See 'd:/Rcompile/CRANpkg/local/3.5/FluMoDL.Rcheck/00install.out' for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
Found the following significant warnings:
  Warning: unable to re-encode 'diffseries.R' line 42
See 'd:/Rcompile/CRANpkg/local/3.5/fracdiff.Rcheck/00install.out' for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
lms: no visible global function definition for 'str2lang'
Undefined global functions or variables:
  str2lang
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GeneralizedUmatrix.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.5Mb
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(raster)
  Loading required package: sp
  > library(sp)
  > library(sf)
  Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
  > 
  > test_check("geometr")
  Loading required package: geometr
  -- 1. Failure: transform from geom to grob (@test_gc_grob.R#25)  ---------------
  Check on names(polyGrob[[1]]) isn't true.
  Must be a permutation of set {x,y,id,id.lengths,pathId,pathId.lengths,rule,name,gp,vp}
  
  Reading layer `nc' from data source `D:\temp\Rtmpmc1P7q\RLIBS_32f441d186ac6\sf\shape\nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  == testthat results  ===========================================================
  [ OK: 695 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 1 ]
  1. Failure: transform from geom to grob (@test_gc_grob.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(raster)
  Loading required package: sp
  > library(sp)
  > library(sf)
  Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
  > 
  > test_check("geometr")
  Loading required package: geometr
  -- 1. Failure: transform from geom to grob (@test_gc_grob.R#25)  ---------------
  Check on names(polyGrob[[1]]) isn't true.
  Must be a permutation of set {x,y,id,id.lengths,pathId,pathId.lengths,rule,name,gp,vp}
  
  Reading layer `nc' from data source `D:\temp\Rtmpmc1P7q\RLIBS_32f441d186ac6\sf\shape\nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  == testthat results  ===========================================================
  [ OK: 695 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 1 ]
  1. Failure: transform from geom to grob (@test_gc_grob.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GET.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GGally.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggbeeswarm.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 42-57 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
there is no package called 'magick'
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggdendro.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggforce.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggiraph.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggplot2.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggpolypath.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggrepel.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggridges.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggsci.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggsignif.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggstance.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gifti)
  > 
  > test_check("gifti")
  trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  -- 1. Error: reading gifti files (@test-reader.R#3)  ---------------------------
  cannot open URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
  Backtrace:
   1. gifti::download_gifti_data(tdir)
   2. utils::download.file(url = url, destfile = destfile)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: reading gifti files (@test-reader.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
Quitting from lines 43-46 (Reading_GIFTI_Files.Rmd) 
Error: processing vignette 'Reading_GIFTI_Files.Rmd' failed with diagnostics:
cannot open URL 'http://johnmuschelli.com/gifti/BV_GIFTI.tar.gz'
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GJRM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: possible error in 'glmnet(glmnet.data$x, ': unused argument (trace.it = trace.it) 
See 'd:/Rcompile/CRANpkg/local/3.5/glmnetcr.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
glmnetcr: possible error in glmnet(glmnet.data$x, glmnet.data$y, family
  = "binomial", weights = glmnet.data$weights, offset = offset, alpha =
  alpha, nlambda = nlambda, lambda.min.ratio = lambda.min.ratio, lambda
  = lambda, standardize = standardize, thresh = thresh, dfmax = dfmax,
  pmax = pmax, exclude = exclude, penalty.factor = c(penalty.factor,
  rep(0, k - 1)), maxit = maxit, type.gaussian = ifelse(nvars < 500,
  "covariance", "naive"), trace.it = trace.it, type.logistic =
  type.logistic): unused argument (trace.it = trace.it)
Running examples in 'glmnetcr-Ex.R' failed
The error most likely occurred in:

> ### Name: coef.glmnetcr
> ### Title: Extract All Model Coefficients
> ### Aliases: coef.glmnetcr
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(diabetes)
> x <- diabetes[, 2:dim(diabetes)[2]]
> y <- diabetes$y
> glmnet.fit <- glmnetcr(x, y)
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights,  : 
  unused argument (trace.it = trace.it)
Calls: glmnetcr
Execution halted
Error in re-building vignettes:
  ...
Loading required package: glmnet
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-18


Error: processing vignette 'glmnetcr.Rnw' failed with diagnostics:
 chunk 2 
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights,  : 
  unused argument (trace.it = trace.it)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/glmnet.Rcheck/00install.out' for details.
Missing or unexported object: 'glmnet::relax.glmnet'
Running examples in 'glmnetUtils-Ex.R' failed
The error most likely occurred in:

> ### Name: cv.glmnet
> ### Title: Formula interface for elastic net cross-validation with
> ###   cv.glmnet
> ### Aliases: cv.glmnet cv.glmnet.default cv.glmnet.formula
> ###   predict.cv.glmnet.formula coef.cv.glmnet.formula
> ###   print.cv.glmnet.formula predict.cv.relaxed.formula
> ###   coef.cv.relaxed.formula
> 
> ### ** Examples
> 
> cv.glmnet(mpg ~ ., data=mtcars)
Error in glmnet(x, y, weights = weights, offset = offset, lambda = lambda,  : 
  unused arguments (gamma = gamma, relax = relax)
Calls: cv.glmnet -> cv.glmnet.formula -> <Anonymous>
Execution halted
Found the following significant warnings:
  Note: possible error in 'RNGkind(sample.kind = "default")': unused argument (sample.kind = "default") 
See 'd:/Rcompile/CRANpkg/local/3.5/gofCopula.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
gof: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofCheckTime: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofCustomTest: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofHybrid: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofKendallCvM: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofKendallKS: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofKernel: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofPIOSRn: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofPIOSTn: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofRosenblattChisq: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofRosenblattGamma: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofRosenblattSnB: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofRosenblattSnC: possible error in RNGkind(sample.kind = "default"):
  unused argument (sample.kind = "default")
gofSn: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofWhite: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
gofco: possible error in RNGkind(sample.kind = "default"): unused
  argument (sample.kind = "default")
Packages suggested but not available for checking:
  'taxstats' 'taxstats1516'
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-35\unhbox\voidb@x \penalty \@M \ {}1.
3/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Determining mirror for Project Gutenberg from http://www.gutenberg.org/robot/harvest
Using mirror https://cand.pglaf.org
Warning in .f(.x[[i]], ...) :
  Could not download a book at https://cand.pglaf.org/7/6/768/768.zip
Warning: Unknown or uninitialised column: 'text'.
Warning in .f(.x[[i]], ...) :
  Could not download a book at https://cand.pglaf.org/7/6/768/768.zip
Warning in .f(.x[[i]], ...) :
  Could not download a book at https://cand.pglaf.org/1/2/6/1260/1260.zip
Quitting from lines 78-81 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Column `gutenberg_id` must be length 0 (the number of rows) or one, not 2
Execution halted
Package required and available but unsuitable version: 'glmnet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/HLMdiag.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/htmlwidgets.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'data.R' line 27
See 'd:/Rcompile/CRANpkg/local/3.5/humidity.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: nnet
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 158-167 (HydeNetPlots.Rmd) 
Error: processing vignette 'HydeNetPlots.Rmd' failed with diagnostics:
Blackjack rules URL does not exist.  Find a new link
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/iBreakDown.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   1.4Mb
    libs   2.4Mb
Depends: includes the non-default packages:
  'lattice' 'caTools' 'gdata' 'gtools' 'gplots' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   8.7Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Running examples in 'iRefR-Ex.R' failed
The error most likely occurred in:

> ### Name: convert_MITAB_to_edgeList
> ### Title: Convert MITAB format to edgeList format
> ### Aliases: convert_MITAB_to_edgeList
> 
> ### ** Examples
> 
>      ## get tables
>      irefindex_curr_ecoli = get_irefindex("562", "13.0", tempdir())
Downloading iRefIndex file...
trying URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Warning in download.file(url, destfile = zipfile) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(url, destfile = zipfile) : 
  cannot open URL 'http://irefindex.org/download/irefindex/data/archive/release_13.0/psi_mitab/MITAB2.6/562.mitab.08122013.txt.zip'
Calls: get_irefindex -> download.file
Execution halted
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking:
  'gurobi' 'Rcplex' 'cplexAPI'
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.3Mb
Error in re-building vignettes:
  ...
Quitting from lines 130-135 (competing-risks.Rmd) 
Error: processing vignette 'competing-risks.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Undocumented code objects:
  'tidy.glht' 'tidy.summary.glht'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking:
  'koRpus.lang.de' 'koRpus.lang.es' 'koRpus.lang.fr' 'koRpus.lang.it'
  'koRpus.lang.ru'

Package which this enhances but not available for checking: 'rkward'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/LambertW.Rcheck/00install.out' for details.
Problems with news in 'inst/NEWS.Rd':
  inst/NEWS.Rd:10: unknown macro '\proglang'
  inst/NEWS.Rd:47: unknown macro '\proglang'
  inst/NEWS.Rd:69: unknown macro '\proglang'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Depends: includes the non-default packages:
  'sn' 'moments' 'BB' 'Bolstad2' 'optimx' 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in 'LilRhino-Ex.R' failed
The error most likely occurred in:

> ### Name: Random_Brains
> ### Title: Random Brains: Neural Network Implementation of Random Forest
> ### Aliases: Random_Brains
> 
> ### ** Examples
> 
> 
> dat = Cross_val_maker(iris, .2)
> 
> train = dat$Train
> test = dat$Test
> 
> Final_Test = Random_Brains(train[,-5],
+   train$Species, as.matrix(test[,-5]),
+   variables = 3, brains = 2)
Warning: Algorithm did not converge in 1 of 1 repetition(s) within the stepmax.
Error in cbind(1, pred) %*% weights[[num_hidden_layers + 1]] : 
  requires numeric/complex matrix/vector arguments
Calls: Random_Brains -> apply -> predict -> predict.nn
Execution halted
split_along_dim: no visible global function definition for 'asplit'
Undefined global functions or variables:
  asplit
Running examples in 'listarrays-Ex.R' failed
The error most likely occurred in:

> ### Name: map_along_dim
> ### Title: Apply a function across subsets along an array dimension
> ### Aliases: map_along_dim map_along_rows map_along_cols
> 
> ### ** Examples
> 
> X <- matrix2(letters[1:15], ncol = 3)
> 
> apply(X, 1, function(x) paste(x, collapse = ""))   # simplifies to a vector
[1] "abc" "def" "ghi" "jkl" "mno"
> map_along_dim(X, 1, ~paste(.x, collapse = ""))     # returns a list
Error in asplit(as.array(X), which_dim) : 
  could not find function "asplit"
Calls: map_along_dim -> lapply -> split_along_dim
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(listarrays)
  > 
  > test_check("listarrays")
  -- 1. Error: specifying `which_dim` by name works (@test-dimnames.R#68)  -------
  could not find function "asplit"
  Backtrace:
   1. testthat::expect_identical(...)
   4. listarrays::split_along_dim(x, "axis2")
  
  -- 2. Error: map_along_dim (@test-map.R#8)  ------------------------------------
  could not find function "asplit"
  Backtrace:
   1. testthat::expect_identical(...)
   4. listarrays::map_along_rows(A, ~paste(.x, collapse = ""))
   5. listarrays::map_along_dim(X, 1L, .f, ...)
   7. listarrays::split_along_dim(X, .dim)
  
  -- 3. Error: split_along_dim (@test-split.R#6)  --------------------------------
  could not find function "asplit"
  Backtrace:
   1. testthat::expect_length(split_along_dim(x, d), dim(x)[d])
   4. listarrays::split_along_dim(x, d)
  
  -- 4. Error: split* works recursively (@test-split.R#30)  ----------------------
  could not find function "asplit"
  Backtrace:
   1. listarrays::split_along_rows(list(x1, x2, x3))
   2. listarrays::split_along_dim(X, 1L, depth = depth)
   3. base::lapply(...)
   4. listarrays:::FUN(X[[i]], ...)
   5. listarrays::split_along_dim(x, which_dim, depth = depth - 1L)
  
  == testthat results  ===========================================================
  [ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: specifying `which_dim` by name works (@test-dimnames.R#68) 
  2. Error: map_along_dim (@test-map.R#8) 
  3. Error: split_along_dim (@test-split.R#6) 
  4. Error: split* works recursively (@test-split.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.2Mb
    testdata   1.6Mb
Error in re-building vignettes:
  ...
Warning in mable(Vaal.Flow$Flow, M = c(2, 100), interval = c(0, 3000), IC = "all",  :
  The maximum candidate degree has been reached 
 with a p-value of the change-point 0.000000.
Warning in mable.ph(cbind(futime1, futime2) ~ age, data = ovarian2, M = c(2,  :
  
The maximum candidate degree has been reached 
with a p-value of the change-point 0.008885.
Warning in mable.ph(formula, data, M, g, pi0, tau, x0, controls, progress) :
  
The maximum candidate degree has been reached 
with a p-value of the change-point 0.008885.
Quitting from lines 370-372 (mable.Rmd) 
Error: processing vignette 'mable.Rmd' failed with diagnostics:
object 'Surv(Y, status)' not found
Execution halted
DomainError: no visible global function definition for 'errorCondition'
fget0: no visible global function definition for 'str2lang'
Undefined global functions or variables:
  errorCondition str2lang
Running examples in 'MachineShop-Ex.R' failed
The error most likely occurred in:

> ### Name: MLModel
> ### Title: MLModel Class Constructor
> ### Aliases: MLModel
> 
> ### ** Examples
> 
> ## Logistic regression model
> LogisticModel <- MLModel(
+   name = "LogisticModel",
+   response_types = "binary",
+   fit = function(formula, data, weights, ...) {
+     glm(formula, data = data, weights = weights, family = binomial, ...)
+   },
+   predict = function(object, newdata, ...) {
+     predict(object, newdata = newdata, type = "response")
+   },
+   varimp = function(object, ...) {
+     pchisq(coef(object)^2 / diag(vcov(object)), 1)
+   }
+ )
> 
> library(MASS)
> res <- resample(type ~ ., data = Pima.tr, model = LogisticModel)
Error in str2lang(x) : could not find function "str2lang"
Calls: resample ... resample.ModelFrame -> .resample -> getMLObject -> fget -> fget0
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MachineShop)
  > 
  > test_check("MachineShop")
  -- 1. Error: (unknown) (@test-ML_StackedModel.R#3)  ----------------------------
  could not find function "str2lang"
  Backtrace:
   1. MachineShop::StackedModel(GBMModel, GLMNetModel(lambda = 0.01))
   2. MachineShop:::getMLObject(control, "MLControl")
   3. MachineShop:::fget(x)
   4. MachineShop:::fget0(x)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 67 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-ML_StackedModel.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: Removed 70 rows containing missing values (geom_point).
Quitting from lines 185-190 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
could not find function "str2lang"
Execution halted
Error in re-building vignettes:
  ...
Package:  markovchain
Version:  0.8.0
Date:     2019-09-13
BugReport: http://github.com/spedygiorgio/markovchain/issues

Loading required package: TraMineR

TraMineR stable version 2.0-13 (Built: 2019-12-14)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.

Loading required package: colorspace
! LaTeX Error: Option clash for package hyperref.

Error: processing vignette 'an_introduction_to_markovchain_package.Rmd' failed with diagnostics:
Failed to compile an_introduction_to_markovchain_package.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See an_introduction_to_markovchain_package.log for more info.
Execution halted
Running examples in 'matrixpls-Ex.R' failed
The error most likely occurred in:

> ### Name: estimator
> ### Title: Parameter estimation of a model matrix
> ### Aliases: estimator estimator.ols estimator.tsls estimator.plscLoadings
> ###   estimator.efaLoadings estimator.cfaLoadings estimator.plsreg
> 
> ### ** Examples
> 
> # Run the education example from the book
> 
> # Sanchez, G. (2013) PLS Path Modeling with R
> # Trowchez Editions. Berkeley, 2013. 
> # http://www.gastonsanchez.com/PLS Path Modeling with R.pdf
> 
> education <- read.csv("http://www.gastonsanchez.com/education.csv")
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> file
Execution halted
Running 'testthat.R' [117s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  -- 1. Error: row eq col on 0 dimension matrix xs and ys (@test-col-versions.R#11
  subscript out of bounds
  Backtrace:
   1. testthat::expect_equal(row_cosinor(X, t), col_cosinor(X, t))
   4. matrixTests::row_cosinor(X, t)
   6. base::`[<-.data.frame`(`*tmp*`, w2 | w3 | w6, c("f", "p"), value = NA)
  
  -- 2. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cas
  subscript out of bounds
  Backtrace:
   1. testthat::expect_equal(...)
   5. matrixTests::row_cosinor(x = x, t = numeric())
   7. base::`[<-.data.frame`(`*tmp*`, w2 | w3 | w6, c("f", "p"), value = NA)
  
  == testthat results  ===========================================================
  [ OK: 2096 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 2 ]
  1. Error: row eq col on 0 dimension matrix xs and ys (@test-col-versions.R#115) 
  2. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cases.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
surfacePlot : <anonymous>: no visible global function definition for
  'hcl.colors'
Undefined global functions or variables:
  hcl.colors
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'MASS' 'boot' 'RColorBrewer' 'scatterplot3d' 'tcltk' 'tcltk2'
  'tkrplot' 'rpanel' 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/mdsOpt.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...
Quitting from lines 128-129 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'magick'
Execution halted
Packages suggested but not available for checking: 'doMC' 'doSMP'
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   1.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Depends: includes the non-default packages:
  'mlr3' 'mlr3db' 'mlr3filters' 'mlr3learners' 'mlr3pipelines'
  'mlr3tuning' 'mlr3viz' 'paradox'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MMVBVS.Rcheck/00install.out' for details.
Running examples in 'mnj-Ex.R' failed
The error most likely occurred in:

> ### Name: flex
> ### Title: FlexBoost
> ### Aliases: flex
> ### Keywords: FlexBoost
> 
> ### ** Examples
> 
> data <- read.csv(url("http://bit.ly/flex_iris"), TRUE)
Warning in open.connection(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in open.connection(file, "rt") : cannot open the connection
Calls: read.csv -> read.table -> open -> open.connection
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MplusAutomation.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/MSCMT.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'dfgps.R' line 51
  Warning: unable to re-encode 'msgps.R' line 98
  Warning: unable to re-encode 'plot.msgps.R' line 60
  Warning: unable to re-encode 'print.msgps.R' line 36
  Warning: unable to re-encode 'summary.msgps.R' line 45
See 'd:/Rcompile/CRANpkg/local/3.5/msgps.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning: unable to access index for repository http://cran.us.r-project.org/src/contrib:
  cannot open URL 'http://cran.us.r-project.org/src/contrib/PACKAGES'
Warning: package 'R.utils' is not available (for R version 3.5.3)
Warning: unable to access index for repository http://cran.us.r-project.org/bin/windows/contrib/3.5:
  cannot open URL 'http://cran.us.r-project.org/bin/windows/contrib/3.5/PACKAGES'
Quitting from lines 18-121 (muHVT.Rmd) 
Error: processing vignette 'muHVT.Rmd' failed with diagnostics:
there is no package called 'R.utils'
Execution halted
Package required and available but unsuitable version: 'pcaMethods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Depends: includes the non-default packages:
  'car' 'pdist' 'pls' 'gplots' 'mvtnorm' 'robustbase' 'gtools' 'bitops'
  'caTools' 'pcaPP' 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NCA.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 174-175 (NEArender_vignette.Rmd) 
Error: processing vignette 'NEArender_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/NeuralNetTools.Rcheck/00install.out' for details.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         6.9Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NMF.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'lpSolve' 'gdata' 'Hmisc' 'rms' 'geometry' 'psych' 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-1'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-4'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 146-147 (NutrienTrackeR.Rmd) 
Error: processing vignette 'NutrienTrackeR.Rmd' failed with diagnostics:
there is no package called 'magick'
Execution halted
Running examples in 'OData-Ex.R' failed
The error most likely occurred in:

> ### Name: entitySets
> ### Title: Get a list of EntitySets for a web service base on OData
> ### Aliases: entitySets
> 
> ### ** Examples
> 
> entitySets("http://services.odata.org/TripPinRESTierService/?$format=json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: entitySets -> <Anonymous> -> paste -> readLines -> file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(ordinalNet)
  > testthatInst <- require(testthat)
  Loading required package: testthat
  > 
  > if (testthatInst) test_check("ordinalNet")
  -- 1. Error: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#
  unused argument (trace.it = trace.it)
  Backtrace:
   1. glmnetcr::glmnetcr(x, y, alpha = 0.5, lambda = 0.1/2, method = "forward")
  
  == testthat results  ===========================================================
  [ OK: 33 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Elastic net sratio matches glmnetcr::glmnet.cr (@test-ordinalNet.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [44s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(paletteer)
  > 
  > test_check("paletteer")
  -- 1. Error: colors show up correctly (@test-vdiffr_palette_check.R#91)  -------
  'hcl.colors' is not an exported object from 'namespace:grDevices'
  Backtrace:
    1. vdiffr::expect_doppelganger(package, plot_in_one(package))
    2. vdiffr:::writer(fig, testcase, title)
    4. vdiffr:::print_plot.function(plot, title)
    5. paletteer:::p()
    6. paletteer:::all_names(name)
    7. base::lapply(paste0(package, "::", names_c), paletteer_c, n = 256)
    8. paletteer:::FUN(X[[i]], ...)
    9. paletteer:::gen_fun(name = palette[2], n = n)
   10. paletteer:::pal_gen(n = n)
   11. grDevices::hcl.colors
   12. base::getExportedValue(pkg, name)
  
  == testthat results  ===========================================================
  [ OK: 74 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: colors show up correctly (@test-vdiffr_palette_check.R#91) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'palr-Ex.R' failed
The error most likely occurred in:

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
Error: 'hcl.colors' is not an exported object from 'namespace:grDevices'
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(palr)
  > 
  > test_check("palr")
  -- 1. Error: image pal (@test-basic.R#22)  -------------------------------------
  'hcl.colors' is not an exported object from 'namespace:grDevices'
  Backtrace:
    1. testthat::expect_length(image_pal(1:10), 10)
    4. palr::image_pal(1:10)
   10. grDevices::hcl.colors
   11. base::getExportedValue(pkg, name)
  
  == testthat results  ===========================================================
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: image pal (@test-basic.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 83-87 (palr.Rmd) 
Error: processing vignette 'palr.Rmd' failed with diagnostics:
'hcl.colors' is not an exported object from 'namespace:grDevices'
Execution halted
Undocumented code objects:
  'knit_print.summary.panel_data'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(passt)
  > 
  > test_check("passt")
  -- 1. Failure: updt_winner_weights work if there are equal output
            acti
  updt_winner_weights(c(1, 0), matrix(rep(0.5, 4), nrow = 2), 0.5) not equal to matrix(c(0.5, 0.75, 0.5, 0.25), nrow = 2).
  4/4 mismatches (average diff: 0.25)
  [1] 0.75 - 0.50 ==  0.25
  [2] 0.50 - 0.75 == -0.25
  [3] 0.25 - 0.50 == -0.25
  [4] 0.50 - 0.25 ==  0.25
  
  -- 2. Failure: sim 1 produces same results as before (@test-simulation.R#11)  --
  `sim1_weights` not equal to `sim1_weights_before`.
  100/100 mismatches (average diff: 0.0485)
  [1] 0.0802 - 0.0698 ==  0.01047
  [2] 0.0608 - 0.0594 ==  0.00139
  [3] 0.0891 - 0.1461 == -0.05699
  [4] 0.0654 - 0.0765 == -0.01101
  [5] 0.0690 - 0.0804 == -0.01134
  [6] 0.0771 - 0.0737 ==  0.00340
  [7] 0.0866 - 0.0627 ==  0.02392
  [8] 0.0637 - 0.0905 == -0.02679
  [9] 0.1463 - 0.0857 ==  0.06061
  ...
  
  -- 3. Failure: sim 4 produces same results as before (@test-simulation.R#26)  --
  `sim4` not equal to `sim4_before`.
  Component "f_dv": Mean relative difference: 0.1759294
  Component "td_dv": Mean relative difference: 0.1087843
  Component "d_dv": Mean relative difference: 0.2325671
  
  == testthat results  ===========================================================
  [ OK: 6 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
  1. Failure: updt_winner_weights work if there are equal output
            activations (@test-helper_functions.R#19) 
  2. Failure: sim 1 produces same results as before (@test-simulation.R#11) 
  3. Failure: sim 4 produces same results as before (@test-simulation.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data      2.5Mb
    doc       1.3Mb
    extdata   9.5Mb
Found the following significant warnings:
  Warning: unable to re-encode 'pq_perf.R' line 1
See 'd:/Rcompile/CRANpkg/local/3.5/pedquant.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 21-35 (artificial_intelligence_evolution.Rmd) 
Error: processing vignette 'artificial_intelligence_evolution.Rmd' failed with diagnostics:
Timeout was reached: [www.onepetro.org] Connection timed out after 10000 milliseconds
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/phateR.Rcheck/00install.out' for details.
Running examples in 'phenocamapi-Ex.R' failed
The error most likely occurred in:

> ### Name: download_midday_images
> ### Title: Downloading the midday images for PhenoCam sites given a time
> ###   range
> ### Aliases: download_midday_images
> 
> ### ** Examples
> 
> 
> download_dir <- download_midday_images('dukehw',
+  y = 2018,
+  months = 2,
+  days=1,
+  download_dir= tempdir())
Warning in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in download.file(url, destfile = tmp_dest, quiet = TRUE, mode = "w") : 
  cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw-midday.txt'
Warning in get_midday_list(site, direct = FALSE) :
  download from the phenocam server was failed
Error in basename(filepaths) : a character vector argument expected
Calls: download_midday_images -> parse_phenocam_filenames -> gsub -> basename
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Error in download.file(url, destfile = tmp, mode = "w") : 
    cannot open URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  -- 1. Error: (unknown) (@testphenocamapi.R#11)  --------------------------------
  file was not found on the server!
  Backtrace:
   1. phenocamapi::get_pheno_ts(...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testphenocamapi.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Quitting from lines 200-209 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
file was not found on the server!
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/pkgbuild.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: D:/temp/RtmpUz4m9B/R.INSTALL1e6ac4e1b345b/pksensi/man/compile_model.Rd:16: unknown macro '\proglang'
  Warning: D:/temp/RtmpUz4m9B/R.INSTALL1e6ac4e1b345b/pksensi/man/compile_model.Rd:30: unknown macro '\proglang'
  Warning: D:/temp/RtmpUz4m9B/R.INSTALL1e6ac4e1b345b/pksensi/man/compile_model.Rd:34: unknown macro '\proglang'
See 'd:/Rcompile/CRANpkg/local/3.5/pksensi.Rcheck/00install.out' for details.
prepare_Rd: compile_model.Rd:16: unknown macro '\proglang'
prepare_Rd: compile_model.Rd:30: unknown macro '\proglang'
prepare_Rd: compile_model.Rd:34: unknown macro '\proglang'
aggregate.rankings: no visible global function definition for 'asplit'
Undefined global functions or variables:
  asplit
Error in re-building vignettes:
  ...
Quitting from lines 547-548 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'magick'
Execution halted
raster_alpha: no visible global function definition for 'asplit'
Undefined global functions or variables:
  asplit
Running examples in 'plothelper-Ex.R' failed
The error most likely occurred in:

> ### Name: raster_alpha
> ### Title: Combine a Matrix of Colors and a Matrix of Alpha Values
> ### Aliases: raster_alpha
> 
> ### ** Examples
> 
> # A color matrix
> co=c("red", "yellow", "green", "blue")
> co=rbind(co, co, co)
> # An alpha matrix
> alp=c(1, 0.6, 0.3, 0.1)
> alp=rbind(alp, alp, alp)
> # Now combine the two
> result=raster_alpha(co, alp)
Error in asplit(color, 2) : could not find function "asplit"
Calls: raster_alpha
Execution halted
Error in re-building vignettes:
  ...
Error in loadVignetteBuilder(vigns$pkgdir) : 
  vignette builder 'knitr' not found
Calls: buildVignettes -> loadVignetteBuilder
Execution halted
Running 'testthat.R' [239s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(portalr)
  > 
  > test_check("portalr")
  -- 1. Error: (unknown) (@test-11-phenocam.R#4)  --------------------------------
  cannot open the connection
  Backtrace:
   1. portalr::phenocam("daily", path = portal_data_path)
   5. utils::read.csv(...)
   6. utils::read.table(...)
   8. base::open.connection(file, "rt")
  
  -- 2. Error: data generated by default setting is same (phenocam)  -------------
  cannot open the connection
  Backtrace:
   1. portalr::phenocam(path = portal_data_path)
   5. utils::read.csv(...)
   6. utils::read.table(...)
   8. base::open.connection(file, "rt")
  
  == testthat results  ===========================================================
  [ OK: 189 | SKIPPED: 10 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: (unknown) (@test-11-phenocam.R#4) 
  2. Error: data generated by default setting is same (phenocam) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In if (all(i == 0L)) stop(gettextf("'arg' should be one of %s",  :
    closing unused connection 4 (http://phenocam.sr.unh.edu/data/archive/portal/ROI/portal_SH_1000_1day.csv)
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/POUMM.Rcheck/00install.out' for details.
Running 'test-all.R' [6s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # Copyright 2015-2019 Venelin Mitov
  > #
  > # This file is part of POUMM.
  > #
  > # POUMM is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # POUMM is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with POUMM  If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
  
  This application has requested the Runtime to terminate it in an unusual way.
  Please contact the application's support team for more information.
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  external pointer is not valid
Running 'test-all.R' [5s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > # Copyright 2015-2019 Venelin Mitov
  > #
  > # This file is part of POUMM.
  > #
  > # POUMM is free software: you can redistribute it and/or modify
  > # it under the terms of the GNU General Public License as published by
  > # the Free Software Foundation, either version 3 of the License, or
  > # (at your option) any later version.
  > #
  > # POUMM is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with POUMM  If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
  
  This application has requested the Runtime to terminate it in an unusual way.
  Please contact the application's support team for more information.
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  external pointer is not valid
Error in re-building vignettes:
  ...

This application has requested the Runtime to terminate it in an unusual way.
Please contact the application's support team for more information.
terminate called after throwing an instance of 'Rcpp::exception'
  what():  external pointer is not valid
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/PPtreeViz.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'preputils.Rmd' failed with diagnostics:
Scanner error: while parsing a quoted scalar at line 3, column 7 found unknown escape character at line 10, column 4
Execution halted
Running examples in 'prismatic-Ex.R' failed
The error most likely occurred in:

> ### Name: clr_grayscale
> ### Title: Transform colors to greyscale
> ### Aliases: clr_grayscale clr_greyscale
> 
> ### ** Examples
> 
> 
> plot(clr_grayscale(rainbow(10)))
> 
> plot(clr_grayscale(terrain.colors(10)))
> 
> plot(clr_grayscale(hcl.colors(10), method = "luma"))
Error in hcl.colors(10) : could not find function "hcl.colors"
Calls: plot -> clr_grayscale -> color
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/probhat.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.5/Quartet.Rcheck/
vign_test/Quartet/vignettes/Critical-distances_files/figure-latex/Plot\%20trees
-1.pdf' not found.

Error: processing vignette 'Critical-distances.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.5/Quartet.Rcheck/vign_test/Quartet/vignettes/Critical-distances.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See Critical-distances.log for more info.
Execution halted
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/randstr.Rcheck/00install.out' for details.
'%<-%'
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running examples in 'rcv-Ex.R' failed
The error most likely occurred in:

> ### Name: import_data
> ### Title: Imports election data
> ### Aliases: import_data
> 
> ### ** Examples
> 
> import_data("http://www.sfelections.org/results/20161108/data/20161206/20161206_masterlookup.txt",
+  header = FALSE)
`curl` package not installed, falling back to using `url()`
Warning in open.connection(con, "rb") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in open.connection(con, "rb") : cannot open the connection
Calls: import_data ... datasource_connection -> read_connection -> open -> open.connection
Execution halted
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
grid object contains more than 10000 pixels
increase `maxpixels` for a finer resolution
Quitting from lines 523-533 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
stopping download
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(retrosheet)
  
  For Retrosheet data obtained with this package:
  
  The information used here was obtained free of charge from
  and is copyrighted by Retrosheet. Interested parties may
  contact Retrosheet at "www.retrosheet.org"
  
  > 
  > test_check("retrosheet")
  -- 1. Error: getParkIDs returns the right results (@test-getParkIDs.R#2)  ------
  cannot open the connection
  Backtrace:
   1. retrosheet::getParkIDs()
   2. base::scan(u, nlines = 1L, nmax = 2L, what = "", sep = ",", quiet = TRUE)
   3. base::file(file, "r")
  
  == testthat results  ===========================================================
  [ OK: 30 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: getParkIDs returns the right results (@test-getParkIDs.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/RIdeogram.Rcheck/00install.out' for details.
Running examples in 'RISmed-Ex.R' failed
The error most likely occurred in:

> ### Name: Cited
> ### Title: Number of citations
> ### Aliases: Cited
> 
> ### ** Examples
> 
> res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
> Cited(res)
Warning in readLines(the_url) :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Too Many Requests'
Error in readLines(the_url) : cannot open the connection
Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
Execution halted
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Rmagic.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'special-fun.R' lines 409, 410, 411
See 'd:/Rcompile/CRANpkg/local/3.5/Rmpfr.Rcheck/00install.out' for details.
Running 'spelling.R' [0s]
  Running 'test-all.R' [243s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library("testthat")
  > Sys.setenv("_R_CHECK_LENGTH_1_CONDITION_" = TRUE)
  > test_check("RNeXML")
  Loading required package: RNeXML
  Loading required package: ape
  -- 1. Error: We can extract tree and trait data to run fitContinuous and fitDisc
  Unknown states 0 not allowed in states vector
  Backtrace:
   1. geiger::fitDiscrete(tree, traits[2], ncores = 1)
   2. geiger::mkn.lik(...)
   3. geiger:::.make.cache.mkn(...)
   4. geiger:::.check.states(tree, states, strict.vals = 1:k)
  
  Namespace prefix xhtml on div is not defined
  Done simulation(s).
  == testthat results  ===========================================================
  [ OK: 626 | SKIPPED: 2 | WARNINGS: 7 | FAILED: 1 ]
  1. Error: We can extract tree and trait data to run fitContinuous and fitDiscrete (@test_comp_analysis.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: ape
Quitting from lines 164-167 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Unknown states 0 not allowed in states vector
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R  11.0Mb
Error in re-building vignettes:
  ...

 google.com                      No encoding supplied: defaulting to UTF-8.



 google.com                      No encoding supplied: defaulting to UTF-8.



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 123-128 (using_robotstxt.Rmd) 
Error: processing vignette 'using_robotstxt.Rmd' failed with diagnostics:
Failed to connect to wikipedia.org port 80: Timed out
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R       3.3Mb
    libs    1.8Mb
    tests   1.3Mb
Error in re-building vignettes:
  ...
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB


Error: processing vignette 'rscala.Rnw' failed with diagnostics:
 chunk 7 (label = Instantiate a bridge for this document) 
Error in scalaConnect(details) : Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>


Execution halted
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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.
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.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> ### Name: SolrList-class
> ### Title: SolrList
> ### Aliases: class:SolrList SolrList-class length,SolrList-method
> ###   names,SolrList-method [<-,SolrList,ANY,ANY,ANY-method
> ###   [[,SolrList,ANY-method [,SolrList-method [[,SolrList-method
> ###   [[<-,SolrList-method unique,SolrList-method searchDocs
> ###   searchDocs,Solr SolrList coerce,Solr,SolrList-method
> ###   coerce,SolrList,DocCollection-method show,SolrList-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  2.22 0.13 2.34 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rstanarm.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Creating a 'stanmodel' object beta_binomial
Quitting from lines 200-208 (external.Rmd) 
Quitting from lines 200-208 (external.Rmd) 
Error: processing vignette 'external.Rmd' failed with diagnostics:
invalid connection
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/rstap.Rcheck/00install.out' for details.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R Under development (unstable) (2017-12-30 r73992)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

Matrix products: default

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

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

other attached packages:
[1] RSVGTipsDevice_1.0-7

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Found the following significant warnings:
  Warning: unable to re-encode 'generics.R' lines 147, 186
See 'd:/Rcompile/CRANpkg/local/3.5/rTorch.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'vkGetAds.R' lines 119, 123
  Warning: unable to re-encode 'vkGetDbRegions.R' line 12
  Warning: unable to re-encode 'vkGetGroupStatPostReach.R' line 37
See 'd:/Rcompile/CRANpkg/local/3.5/rvkstat.Rcheck/00install.out' for details.
Undocumented code objects:
  'type_sum.rxRateDur'
All user-level objects in a package should have documentation entries.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running examples in 'sae2-Ex.R' failed
The error most likely occurred in:

> ### Name: geo_ratios
> ### Title: Compute rates or ratios for a set of geographic entities over a
> ###   set of years
> ### Aliases: geo_ratios
> 
> ### ** Examples
> 
> require(survey)
> require(MASS)
> D <- 20 # number of domains
> T <- 5 # number of years
> samp <- 16 # number of sample cases per domain
> set.seed(1)
> # use conditional.mean=TRUE to generate true small area values
> # without sampling error
> Y.list <- mvrnormSeries(D=D, T=T, rho.dyn=.9, sigma.v.dyn=1, 
+    sigma.u.dyn=.19, sigma.e=diag(5), conditional.mean=TRUE)
> # generate sampling errors
> e <- rnorm(samp * T * D, mean=0, sd=4)
> Y <- Y.list[[2]] + tapply(e, rep(1:100, each=16), mean) 
> data <- data.frame(Y=Y, X=rep(1:T, times=D))
> # model fit with the true sampling variances
> result.dyn  <- eblupDyn(Y ~ X, D, T, vardir = diag(100), data=data)
Error in y - X %*% B_Est : non-conformable arrays
Calls: eblupDyn -> dynRYfit
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 85-92 (user-defined-design.Rmd) 
Error: processing vignette 'user-defined-design.Rmd' failed with diagnostics:
task 1 failed - "no method or default for coercing "matrix" to "dgCMatrix""
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   1.9Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'pogs'
Error in re-building vignettes:
  ...
Quitting from lines 24-62 (scriptexec.Rmd) 
Error: processing vignette 'scriptexec.Rmd' failed with diagnostics:
grepl("command1", output$output) not equal to TRUE.
1 element mismatch
Execution halted
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/SmartEDA.Rcheck/00install.out' for details.
prepare_Rd: maxsel.rd:27-29: Dropping empty section \details
prepare_Rd: transf.inter.rd:23-25: Dropping empty section \details
Error in re-building vignettes:
  ...
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

! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.5/SongEvo.Rcheck/
vign_test/SongEvo/vignettes/SongEvo_files/figure-latex/Examine\%20population\%2
0size\%20over\%20time-1.pdf' not found.

Error: processing vignette 'SongEvo.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.5/SongEvo.Rcheck/vign_test/SongEvo/vignettes/SongEvo.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See SongEvo.log for more info.
Execution halted
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.2Mb
    libs   1.2Mb
uniquemap.matrix: no visible global function definition for 'asplit'
Undefined global functions or variables:
  asplit
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
prepare_Rd: H.Binv.Rd:48-50: Dropping empty section \note
prepare_Rd: V.theta.Rd:28-30: Dropping empty section \details
prepare_Rd: V.theta.Rd:43-45: Dropping empty section \note
prepare_Rd: V.theta.Rd:49-51: Dropping empty section \seealso
prepare_Rd: V.theta.Rd:52-53: Dropping empty section \examples
prepare_Rd: confid.int.theta.Rd:62-64: Dropping empty section \note
prepare_Rd: dd.est.Rd:39-41: Dropping empty section \note
prepare_Rd: dd.est.Rd:45-47: Dropping empty section \seealso
prepare_Rd: ell.theta.Rd:60-62: Dropping empty section \note
prepare_Rd: ell.theta.Rd:69-70: Dropping empty section \examples
prepare_Rd: grad.hessinv.Rd:47-49: Dropping empty section \note
prepare_Rd: ks.sporm.Rd:43-45: Dropping empty section \note
prepare_Rd: ks.stat.Rd:39-41: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:66-68: Dropping empty section \note
prepare_Rd: mrle.sporm.Rd:72-74: Dropping empty section \seealso
prepare_Rd: newton.theta.Rd:47-49: Dropping empty section \note
prepare_Rd: phi.Rd:32-38: Dropping empty section \value
prepare_Rd: phi.Rd:48-50: Dropping empty section \note
prepare_Rd: plotor.Rd:26-32: Dropping empty section \value
prepare_Rd: plotor.Rd:42-44: Dropping empty section \note
prepare_Rd: plotor.Rd:48-50: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:53-54: Dropping empty section \seealso
prepare_Rd: sporm-package.Rd:55-56: Dropping empty section \examples
prepare_Rd: test.theta.Rd:54-56: Dropping empty section \note
prepare_Rd: elltheta.rd:53-55: Dropping empty section \note
prepare_Rd: elltheta.rd:62-63: Dropping empty section \examples
Running 'testthat.R' [244s]
Running the tests in 'tests/testthat.R' failed.
Complete 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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/StereoMorph.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
stm v1.3.5 successfully loaded. See ?stm for help. 
 Papers, resources, and other materials at structuraltopicmodel.com
Warning in load(url("http://goo.gl/VPdxlS")) :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'

Error: processing vignette 'stmVignette.Rnw' failed with diagnostics:
 chunk 7 
Error in load(url("http://goo.gl/VPdxlS")) : cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
Warning: Removed 1 rows containing missing values (geom_path).
Quitting from lines 904-907 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
there is no package called 'ggthemes'
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.3Mb
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  Backtrace:
   1. testthat::expect_true(process_exists(child_id))
   4. subprocess::process_exists(child_id)
   5. base::isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  [ OK: 58 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  Backtrace:
   1. testthat::expect_true(process_exists(child_id))
   4. subprocess::process_exists(child_id)
   5. base::isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  [ OK: 58 | SKIPPED: 3 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_tibble.grouped_df', 'as_tibble.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/survMisc.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  -- 1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  cannot open URL 'http://www.europarl.europa.eu/oeil/popups/printfichetechnical.pdf?id=673511&lang=fr'
  Backtrace:
   1. tabulizer::extract_text(f2, page = 1, encoding = "latin1")
   2. tabulizer:::load_doc(file, password = password, copy = copy)
   3. tabulizer:::localize_file(path = file, copy = copy)
   4. utils::download.file(path, tmp, quiet = quiet, mode = "wb")
  
  == testthat results  ===========================================================
  [ OK: 89 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: Read French language PDF w/correct encoding (@test_non-latin.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
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 3.6.1, GDAL 2.2.3, PROJ 4.9.3
> 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
Package required but not available: 'dipsaus'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [128s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # This is necessary because some tests fail otherwise; see https://github.com/hadley/testthat/issues/144
  > Sys.setenv("R_TESTS" = "")
  > 
  > library(testthat)
  > library(tidybayes)
  > 
  > test_check("tidybayes")
  -- 1. Failure: [add_]predicted_draws works on brms models with categorical outco
  predicted_draws(m_cyl_mpg, mtcars_tbl, seed = 1234, n = 100) not equal to `ref`.
  Incompatible type for column `.prediction`: x numeric, y factor
  
  -- 2. Failure: [add_]predicted_draws works on brms models with categorical outco
  add_predicted_draws(mtcars_tbl, m_cyl_mpg, seed = 1234, n = 100) not equal to `ref`.
  Incompatible type for column `.prediction`: x numeric, y factor
  
  == testthat results  ===========================================================
  [ OK: 271 | SKIPPED: 41 | WARNINGS: 38 | FAILED: 2 ]
  1. Failure: [add_]predicted_draws works on brms models with categorical outcomes (@test.predicted_draws.R#126) 
  2. Failure: [add_]predicted_draws works on brms models with categorical outcomes (@test.predicted_draws.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: ggplot2
Loading required package: maps
Loading required package: ggrepel
Quitting from lines 62-64 (tidygeocoder.Rmd) 
Error: processing vignette 'tidygeocoder.Rmd' failed with diagnostics:
cannot open URL 'http://nominatim.openstreetmap.org/search?q=Fake+Address&format=xml&polygon=0&addressdetails=0'
Execution halted
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Running 'testthat.R' [51s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(trelliscopejs)
  > 
  > test_check("trelliscopejs")
  -- 1. Error: examples run without barfing (@test-trelliscope.R#140)  -----------
  Can't cast `data$class2` <cog> to `data$class2` <cog>.
  Backtrace:
    1. base::print(p)
   16. vctrs:::vec_cast.integer.integer(...)
   17. vctrs::vec_default_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   18. vctrs::stop_incompatible_cast(x, to, x_arg = x_arg, to_arg = to_arg)
   19. vctrs:::stop_incompatible(...)
   20. vctrs:::stop_vctrs(...)
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 695 | FAILED: 1 ]
  1. Error: examples run without barfing (@test-trelliscope.R#140) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs  12.1Mb
Error in re-building vignettes:
  ...
Quitting from lines 171-210 (TruncatedNormal_vignette.Rmd) 
Error: processing vignette 'TruncatedNormal_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in 'uklr-Ex.R' failed
The error most likely occurred in:

> ### Name: uklr_def
> ### Title: Linked Data Definitions
> ### Aliases: uklr_def ukhp_def ukppd_def uktrans_def
> 
> ### ** Examples
> 
> 
> uklr_def()
Warning in file(file, "rt") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(file, "rt") : cannot open the connection
Calls: uklr_def -> read.csv -> read.table -> file
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 26-29 (UniprotR.Rmd) 
Error: processing vignette 'UniprotR.Rmd' failed with diagnostics:
first argument must be a vector
Execution halted
Packages suggested but not available for checking: 'vaers' 'vaersND'
Error in re-building vignettes:
  ...
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 347-378 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
object 'epi' not found
Execution halted
Running examples in 'vegalite-Ex.R' failed
The error most likely occurred in:

> ### Name: from_spec
> ### Title: Take a JSON Vega-Lite Spec and render as an htmlwidget
> ### Aliases: from_spec
> 
> ### ** Examples
> 
> from_spec("http://rud.is/dl/embedded.json")
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: from_spec -> readLines -> file
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    doc    1.2Mb
    help   2.9Mb
Error in re-building vignettes:
  ...
Loading required package: knitr
Loading required package: wCorr
wCorr v1.9.1

Loading required package: lattice
Loading required package: captioner
! Package pdftex.def Error: File `d:/RCompile/CRANpkg/local/3.5/wCorr.Rcheck/vi
gn_test/wCorr/vignettes/wCorrArguments_files/figure-latex/ML\%20RMSE\%20plot-1.
pdf' not found.

Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
LaTeX failed to compile d:/RCompile/CRANpkg/local/3.5/wCorr.Rcheck/vign_test/wCorr/vignettes/wCorrArguments.tex. See https://yihui.org/tinytex/r/#debugging for debugging tips. See wCorrArguments.log for more info.
Execution halted
Running examples in 'WikidataR-Ex.R' failed
The error most likely occurred in:

> ### Name: extract_claims
> ### Title: Extract Claims from Returned Item Data
> ### Aliases: extract_claims
> 
> ### ** Examples
> 
> # Get item data
> adams_data <- get_item("42")
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Failed to connect to wikidata.org port 80: Timed out
Calls: get_item ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
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
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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in normalizePath(f2) :
  path[1]="webshota48e5a51ffbd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshota48e5a51ffbd.png': No such file or directory
Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.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/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

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/adamethods.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Depends: includes the non-default packages:
  ‘Matrix’ ‘coda’ ‘mvtnorm’ ‘MCMCpack’ ‘spatstat’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Package required but not available: ‘DeconRNASeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
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/ade4TkGUI.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/adiv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning in FUN(X[[i]], ...) :
  no non-missing arguments to max; returning -Inf
Warning: Removed 16 rows containing missing values (geom_point).
Warning: Removed 3 rows containing missing values (geom_errorbar).
Warning in normalizePath(f2) :
  path[1]="webshot6b273aa7c9f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot6b273aa7c9f.png': No such file or directory
Quitting from lines 782-783 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.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/AGHmatrix.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 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.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/AIG.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/akmedoids.Rcheck/00install.out’ for details.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/amap.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AnalyzeFMRI.Rcheck/00install.out’ for details.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    23.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.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/Anthropometry.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

Error in loadNamespace(name) : there is no package called 'BiocManager'
Error in loadNamespace(name) : there is no package called 'devtools'
Error: processing vignette 'help.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
installed size is 93.5Mb
  sub-directories of 1Mb or more:
    libs  93.0Mb
Error in re-building vignettes:
  ...

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
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

Quitting from lines 106-107 (advanced-configuration.Rmd) 
Error: processing vignette 'advanced-configuration.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Returned 'NA'!


No TSN found for species 'Juniperus occidentalis'!


Retrieving data for taxon 'Pinus strobus'





More than one TSN found for taxon 'Pinus strobus'!

            Enter rownumber of taxon (other inputs will return 'NA'):


Returned 'NA'!


No TSN found for species 'Pinus strobus'!


Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/aqr.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/archiDART.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.1Mb
Packages suggested but not available for checking:
  ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
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/Arothron.Rcheck/00install.out’ for details.
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  20.8Mb
record: no visible global function definition for ‘str2lang’
Undefined global functions or variables:
  str2lang
Found the following significant warnings:
  Note: possible error in 'set.seed(100, sample.kind = "Rejection")': unused argument (sample.kind = "Rejection") 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/assignR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/audio.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 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Packages required but not available:
  ‘fgsea’ ‘ConsensusClusterPlus’ ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing or unexported object: ‘grDevices::hcl.colors’
Running examples in ‘babette-Ex.R’ failed
The error most likely occurred in:

> ### Name: prepare_file_creation
> ### Title: Prepare for 'BEAST2' creating files
> ### Aliases: prepare_file_creation
> 
> ### ** Examples
> 
> library(testthat)
> 
> # For a test inference model, the files can be prepared
> inference_model <- create_test_inference_model()
> beast2_options <- create_beast2_options()
> expect_silent(prepare_file_creation(inference_model, beast2_options))
Error in prepare_file_creation(inference_model, beast2_options) : 
  Cannot create file '/Users/urbanek/Library/Caches/beast2_111076b629bfa.xml.state'. 
Maybe no permissions to write there?
Calls: expect_silent ... withCallingHandlers -> withVisible -> eval_bare -> prepare_file_creation
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: beautier
Loading required package: beastier
Loading required package: mauricer
Loading required package: tracerer
Warning in engine$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 44-51 (step_by_step.Rmd) 
Error: processing vignette 'step_by_step.Rmd' failed with diagnostics:
Cannot write to file with name '/Users/urbanek/Library/Caches/beast2_1111c1ccac1c1.xml' 
Perhaps no permission to write there? 
Error message: cannot open the connection 
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.6Mb
installed size is 62.4Mb
  sub-directories of 1Mb or more:
    libs  61.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BAGofT.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/baseflow.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: unable to re-encode ‘baseline.lowpass.R’ line 4
  Warning: unable to re-encode ‘baseline.medianWindow.R’ line 3
  Warning: unable to re-encode ‘baseline.modpolyfit.R’ line 4
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/baseline.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.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [210s/210s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Failure: (unknown) (@test-mcmc.r#45)  ────────────────────────────────────
  mcmc_res1$basket$ESS not equivalent to mcmc_ref2$ESS.
  3/3 mismatches (average diff: 2.09)
  [1] 39.8 - 37.5 == 2.330
  [2] 38.3 - 37.9 == 0.435
  [3] 38.4 - 34.9 == 3.494
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 49 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: (unknown) (@test-mcmc.r#41) 
  2. Failure: (unknown) (@test-mcmc.r#45) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

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/BAT.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 12 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 8 ]
  1. Failure: the MHEdge function returns the correct matrix (@testMCMC.R#68) 
  2. Failure: the MHEdge function returns the correct matrix (@testMCMC.R#69) 
  3. Failure: the MHEdge function returns the correct matrix (@testMCMC.R#71) 
  4. Failure: the MHEdge function returns the correct matrix (@testMCMC.R#72) 
  5. Failure: MHEdge returns the correct matrix with and without pmr (@testMCMCGV.R#53) 
  6. Failure: MHEdge returns the correct matrix with and without pmr (@testMCMCGV.R#54) 
  7. Failure: MHEdge returns the correct matrix with and without pmr (@testMCMCGV.R#56) 
  8. Failure: MHEdge returns the correct matrix with and without pmr (@testMCMCGV.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bayesCL.Rcheck/00install.out’ for details.
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    libs  49.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BayesLogit.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  16.2Mb
Error in re-building vignettes:
  ...
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.2, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)

Attaching package: 'rstan'

The following object is masked from 'package:R2jags':

    traceplot

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

    traceplot

Quitting from lines 205-211 (getting_started.Rmd) 
Error: processing vignette 'getting_started.Rmd' failed with diagnostics:
unable to load shared object '/tmp/Rtmp6wMLDg/filee19e339cc254.so':
  dlopen(/tmp/Rtmp6wMLDg/filee19e339cc254.so, 6): Library not loaded: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
  Referenced from: /tmp/Rtmp6wMLDg/filee19e339cc254.so
  Reason: Incompatible library version: filee19e339cc254.so requires version 3.6.0 or later, but libR.dylib provides version 3.5.0
Execution halted
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs  13.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bbl.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
installed size is 61.6Mb
  sub-directories of 1Mb or more:
    libs  60.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BetaPASS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BHAI.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BIGL.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="webshot1083e4f229353.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1083e4f229353.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      1.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.1Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
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 40-47 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.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/binomialMix.Rcheck/00install.out’ for details.
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’ ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bioacoustics.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 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘BiocVersion’
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/Biocomb.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/BiodiversityR.Rcheck/00install.out’ for details.
Packages required but not available: ‘ChemmineR’ ‘fmcsR’

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'http://vizjs.org/viz.v1.1.0.min.js'
Content type 'application/javascript' length 23466 bytes (22 KB)
==================================================
downloaded 22 KB

trying URL 'http://vizjs.org/viz.v1.1.0.min.js'
Content type 'application/javascript' length 23466 bytes (22 KB)
==================================================
downloaded 22 KB

Quitting from lines 42-54 (bipartiteD3_Intro.Rmd) 
Error: processing vignette 'bipartiteD3_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 49.9Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
installed size is 32.1Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Running ‘testthat.R’ [39s/39s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 0.8 - 1 == -0.2
  
  ── 2. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#23) 
  ...$NULL not equal to 0.
  1/1 mismatches
  [1] 0.1 - 0 == 0.1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 50 | SKIPPED: 0 | WARNINGS: 1021 | FAILED: 2 ]
  1. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#10) 
  2. Failure: the binomial frequentist RAR output is (@test_binomialfreq.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.7Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BNPTSclust.Rcheck/00install.out’ for details.
Running examples in ‘bnspatial-Ex.R’ failed
The error most likely occurred in:

> ### Name: bnspatial
> ### Title: Spatialize the Bayesian network
> ### Aliases: bnspatial
> 
> ### ** Examples
> 
> list2env(ConwyData, environment())
<environment: R_GlobalEnv>
> 
> network <- LandUseChange
> spatialData <- c(ConwyLU, ConwySlope, ConwyStatus)
> lookup <- LUclasses
> 
> bn <- bnspatial(network, 'FinalLULC', spatialData, lookup)

"CurrentLULC" points to:
 ->  ConwyLU 

With states:
forest    arable    other

Represented by integer values:
2 <-> 3 <-> 1
----------------------------------

"Slope" points to:
 ->  ConwySlope 

With states:
flat    moderate    steep

Discretized by intervals:
-Inf <-> 1 <-> 7 <-> Inf
----------------------------------

"LegalStatus" points to:
 ->  ConwyStatus 

With states:
public    private    protected

Represented by integer values:
4 <-> 3 <-> 1
----------------------------------
Error in NextMethod("compile") : no method to invoke
Calls: bnspatial ... querygrain.grain -> compile -> compile.grain -> NextMethod
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: raster
Loading required package: sp
Quitting from lines 93-114 (bnspatial.Rmd) 
Error: processing vignette 'bnspatial.Rmd' failed with diagnostics:
no method to invoke
Execution halted
installed size is 324.7Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      315.8Mb
installed size is 66.5Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 308-333 (BOSSreg.Rmd) 
Error: processing vignette 'BOSSreg.Rmd' failed with diagnostics:
cannot open the connection to 'https://raw.githubusercontent.com/sentian/BOSSreg/master/r-package/vignettes/realdata.rds'
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/bpca.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified

(R:96230): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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/brainR.Rcheck/00install.out’ for details.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs  39.0Mb
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Stan model 'breath_test_1' does not contain samples.
  Stan model 'breath_test_1' does not contain samples.
  ── 2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@
  arguments imply differing number of rows: 500, 0
  Backtrace:
   1. breathteststan::stan_fit(...)
   2. base::data.frame(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 4 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16) 
  2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21) 
  
  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/briqr.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R     2.9Mb
    doc   2.6Mb
Package suggested but not available for checking: ‘pasilla’
Packages required but not available: ‘DiffBind’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  25.2Mb
installed size is 80.9Mb
  sub-directories of 1Mb or more:
    libs  80.1Mb
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  19.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bwsTools.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

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]="./webshotb3c71d491160.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb3c71d491160.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘cairoDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cairo
> ### Title: The Cairo Graphics Device
> ### Aliases: Cairo Cairo_pdf Cairo_ps Cairo_svg Cairo_png
> ### Keywords: device
> 
> ### ** Examples
> 
> Cairo()

(R:47090): Gdk-CRITICAL **: gdk_screen_get_width: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_width_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_height: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_height_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:47090): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:47090): Gtk-CRITICAL **: gtk_window_set_default_size: assertion `width >= -1' failed

(R:47090): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:47090): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:47090): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: Cairo()
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.4-8, (SVN revision 845)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.4.2, released 2019/06/28
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 5.2.0, September 15th, 2018, [PJ_VERSION: 520]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.3-2 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
This is secr 4.1.0. For overview type ?secr

Attaching package: 'secr'

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

    flip, rotate, shift, trim

Quitting from lines 51-55 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/carat.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = colnames(countData)) : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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

Warning in normalizePath(f2) :
  path[1]="webshot343f5bedf511.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot343f5bedf511.png': No such file or directory
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

     Hanna Meyer, Christoph Reudenbach, Marvin Ludwig, Thomas Nauss
     _Maintainer:_ Hanna Meyer <email: hanna.meyer@geo.uni-marburg.de>


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]="./webshot2c6d78301f9d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2c6d78301f9d.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.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/caTools.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   1.1Mb
    libs      3.1Mb
installed size is 103.9Mb
  sub-directories of 1Mb or more:
    libs  103.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CCAMLRGIS.Rcheck/00install.out’ for details.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.6Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.5Mb
Package required but not available: ‘tlrmvnmvt’

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/centrifugeR.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/cepreader.Rcheck/00install.out’ for details.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: 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/changepoint.np.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘GenomicInteractions’ ‘Gviz’ ‘countreg’
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 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ChillModels.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/chinese.misc.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   3.7Mb
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
Found the following significant warnings:
  Note: possible error in 'trimws(x, which = "both", ': unused argument (whitespace = "[ \t\r\n]") 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clean.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘clean-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean
> ### Title: Clean column data to a class
> ### Aliases: clean clean.data.frame clean_logical clean_factor
> ###   clean_numeric clean_character clean_currency clean_Date clean_POSIXct
> 
> ### ** Examples
> 
> clean_logical(c("Yes", "No"))   # English
[1]  TRUE FALSE
> clean_logical(c("Oui", "Non"))  # French
[1]  TRUE FALSE
> clean_logical(c("ya", "tidak")) # Indonesian
[1]  TRUE FALSE
> clean_logical(x = c("Positive", "Negative", "Unknown", "Some value"),
+               true = "pos", false = "neg")
[1]  TRUE FALSE    NA    NA
> 
> gender_age <- c("male 0-50", "male 50+", "female 0-50", "female 50+")
> clean_factor(gender_age, c("M", "F"))
[1] M M F F
Levels: M F
> clean_factor(gender_age, c("Male", "Female"))
[1] Male   Male   Female Female
Levels: Male Female
> clean_factor(gender_age, c("0-50", "50+"), ordered = TRUE)
[1] 0-50 50+  0-50 50+ 
Levels: 0-50 < 50+
> 
> clean_Date("13jul18", "ddmmmyy")
[1] "2018-07-13"
> clean_Date("12 august 2010")
Cleaning dates using format 'dd mmmm yyyy' ('%d %B %Y')
[1] "2010-08-12"
> clean_Date("12 06 2012")
Cleaning dates using format 'dd mm yyyy' ('%d %m %Y')
[1] "2012-06-12"
> clean_Date(36526) # Excel date
Cleaning dates using Excel format
[1] "2000-01-01"
> clean_Date("43658")
Cleaning dates using Excel format
[1] "2019-07-12"
> clean_Date("14526", "Excel") # "1939-10-08"
[1] "1939-10-08"
> 
> clean_POSIXct("Created log on 2019/04/11 11:23 by user Joe")
[1] "2019-04-11 11:23:00 EDT"
> 
> clean_numeric("qwerty123456")
[1] 123456
> clean_numeric("Positive (0.143)")
[1] 0.143
> clean_numeric("0,143")
[1] 0.143
> 
> clean_character("qwerty123456")
Error in trimws(x, which = "both", whitespace = "[ \t\r\n]") : 
  unused argument (whitespace = "[ \t\r\n]")
Calls: clean_character
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(clean)
  > 
  > test_check("clean")
  ── 1. Error: cleaning works (@test-clean.R#42)  ────────────────────────────────
  unused argument (whitespace = "[ \t\r\n]")
  Backtrace:
   1. testthat::expect_equal(...)
   4. clean::clean_character(values)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 20 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: cleaning works (@test-clean.R#42) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
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 73-75 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
Execution halted
Running ‘testthat.R’ [94s/94s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 785 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 12 ]
  1. Failure: Check randwin output with slidingwin and max (@testrandwin.R#39) 
  2. Failure: Check randwin output with slidingwin and max (@testrandwin.R#41) 
  3. Failure: Check randwin output with slidingwin and mean (@testrandwin.R#85) 
  4. Failure: Check randwin output with slidingwin and mean (@testrandwin.R#87) 
  5. Failure: Check randwin output works with spatial replication (@testrandwin.R#135) 
  6. Failure: Check randwin output works with spatial replication (@testrandwin.R#137) 
  7. Failure: Check randwin output with weightwin (@testrandwin.R#181) 
  8. Failure: Check randwin output with weightwin (@testrandwin.R#182) 
  9. Failure: Check randwin output with weightwin (@testrandwin.R#183) 
  1. ...
  
  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/CliquePercolation.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/clpAPI.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
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/clusterSim.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘InteractionSet’ ‘GenomicFeatures’ ‘GenomicInteractions’
  ‘rtracklayer’ ‘BSgenome.Hsapiens.UCSC.hg19’

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.

Attaching package: 'labelled'

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

    to_factor

Quitting from lines NA-15 (codebook.Rmd) 
Error: processing vignette 'codebook.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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cohorttools.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/CoImp.Rcheck/00install.out’ for details.
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:833: unknown macro '\proglang'
  inst/NEWS.Rd:893: unknown macro '\proglang'
  inst/NEWS.Rd:1034: unknown macro '\proglang'
  inst/NEWS.Rd:1050: unknown macro '\proglang'
  inst/NEWS.Rd:1052: unknown macro '\proglang'
  inst/NEWS.Rd:1057: unknown macro '\proglang'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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/colourvision.Rcheck/00install.out’ for details.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.2Mb
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.6Mb
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Compositional.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   11. pins::board_pin_store(...)
   13. pins:::board_pin_create.local(...)
   14. pins:::pin_registry_update(name = name, component = board$name)
   15. pins:::pin_registry_save_entries(entries, component)
   16. yaml::write_yaml(entries, pin_registry_config(component))
   17. base::file(file, "w", encoding = fileEncoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: tbl pin is created w/o error (@test-pins.R#16) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a 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/ConsRank.Rcheck/00install.out’ for details.
installed size is 46.9Mb
  sub-directories of 1Mb or more:
    libs  45.8Mb
Packages required and available but unsuitable versions:
  ‘methods’ ‘parallel’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/ConvergenceConcepts.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/cops.Rcheck/00install.out’ for details.
Package required but not available: ‘piano’

Package suggested but not available for checking: ‘PharmacoGx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
is_deprecated: no visible global function definition for
  ‘warningCondition’
Undefined global functions or variables:
  warningCondition
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CoSMoS.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CovTools.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Quitting from lines 70-73 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
no applicable method for 'depth' applied to an object of class "NULL"
Execution halted
Error: QuartzBitmap_Output - unable to open file 'figure/unnamed-chunk-4-1.png'
Fatal error: error during cleanup
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 112-132 (COXMEG_example.Rmd) 
Error: processing vignette 'COXMEG_example.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cplexAPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cpsurvsim.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.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 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘clusterProfiler’
Error in re-building vignettes:
  ...
    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

The following object is masked from 'package:R.oo':

    trim


Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
Execution halted
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
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/crs.Rcheck/00install.out’ for details.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is 88.7Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  84.9Mb
Package suggested but not available for checking: ‘tidyrules’
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 12-20 (cubist.Rmd) 
Error: processing vignette 'cubist.Rmd' failed with diagnostics:
there is no package called 'tidyrules'
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   4.2Mb
Package required but not available: ‘flowDensity’

Packages required and available but unsuitable versions:
  ‘Biobase’ ‘graphics’ ‘grDevices’ ‘stats’ ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Error in re-building vignettes:
  ...
Warning in engine$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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [103s/104s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55)  ───────
  df_analysed.result$bca_ci_high not equal to 0.07162217.
  1/1 mismatches
  [1] 0.146 - 0.0716 == 0.0742
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 17 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 5 ]
  1. Failure: Using `grp` as x column is kosher (@test-unquoting.R#50) 
  2. Failure: Using `grp` as x column is kosher (@test-unquoting.R#51) 
  3. Failure: Using `grp` as x column is kosher (@test-unquoting.R#53) 
  4. Failure: Using `grp` as x column is kosher (@test-unquoting.R#54) 
  5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

    filter, lag

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

    intersect, setdiff, setequal, union


********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Warning: `data_frame()` is deprecated, use `tibble()`.
This warning is displayed once per session.
Loading required package: boot
Loading required package: magrittr
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 110-166 (robust-statistical-visualization.Rmd) 
Error: processing vignette 'robust-statistical-visualization.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Packages required and available but unsuitable versions: ‘compiler’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   3.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  55.5Mb
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot69f82cd291ad.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot69f82cd291ad.png': No such file or directory
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Depends: includes the non-default packages:
  ‘xtable’ ‘akima’ ‘R.oo’ ‘R.methodsS3’ ‘matlab’ ‘lattice’ ‘locfit’
  ‘grid’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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.
Joining, by = "key"
Joining, by = "key"
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 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Depends: includes the non-default packages:
  ‘Deducer’ ‘psych’ ‘GPArotation’ ‘mvnormtest’ ‘irr’ ‘klaR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  ‘JavaGD’ ‘Deducer’ ‘sp’ ‘maptools’ ‘OpenStreetMap’ ‘scales’ ‘rgdal’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Delaporte.Rcheck/00install.out’ for details.
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  58.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/depmixS4.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/depth.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/DescTools.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rmosek’ ‘Rsymphony’
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.1Mb
    libs      2.1Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.4Mb
installed size is 50.7Mb
  sub-directories of 1Mb or more:
    libs  50.3Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: rgl
Loading required namespace: rmarkdown
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DHBins.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 57-79 (graphviz-mermaid.Rmd) 
Error: processing vignette 'graphviz-mermaid.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dipsaus.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/Directional.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/directPA.Rcheck/00install.out’ for details.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/distTails.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.4Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   8.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DoE.multi.response.Rcheck/00install.out’ for details.
installed size is 21.5Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Running ‘chisq-nonc-ex.R’ [22s/22s]
  Running ‘dnchisq-tst.R’ [0s/0s]
  Running ‘pnbeta-tst.R’ [0s/0s]
  Running ‘pnt-precision-problem.R’ [11s/11s]
  Running ‘ppois-ex.R’ [1s/1s]
  Running ‘qPoisBinom-ex.R’ [0s/0s]
  Running ‘qbeta-dist.R’ [11s/11s]
  Running ‘qbeta-tst.R’ [0s/0s]
  Running ‘qgamma-ex.R’ [14s/15s]
Running the tests in ‘tests/qgamma-ex.R’ failed.
Last 13 lines of output:
  Warning message:
  In xy.coords(x, y, xlabel, ylabel, log) :
    503 y values <= 0 omitted from logarithmic plot
  > ## gives a *warning* from axis()  because of subnormal y-range  {was error, fixed in R-devel (2018-08)}
  > curve(qgamma(x, .001, lower=FALSE), .52, .53, n=1001, log="y")
  Error in axis(side = side, at = at, labels = labels, ...) : 
    CreateAtVector [log-axis()]: axp[0] = 0 < 0!
  Calls: curve ... plot.default -> localAxis -> Axis -> Axis.default -> axis
  In addition: Warning messages:
  1: In xy.coords(x, y, xlabel, ylabel, log) :
    514 y values <= 0 omitted from logarithmic plot
  2: In plot.window(...) : Internal(pretty()): very small range.. corrected
  3: In axis(side = side, at = at, labels = labels, ...) :
    CreateAtVector "log"(from axis()): axp[0] = 0 !
  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/drugCombo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot11ae36636580c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot11ae36636580c.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
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 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.4Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  21.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.6Mb
Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 0.00667 - 0.01 == -0.00333
  
  ── 2. Failure: multiclass.result (@test_neighborhood.R#16)  ────────────────────
  as.numeric(aux$N4) not equal to 0.00666667.
  1/1 mismatches
  [1] 0.0133 - 0.00667 == 0.00667
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 97 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: multiclass.result (@test_linearity.R#13) 
  2. Failure: multiclass.result (@test_neighborhood.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 67.6Mb
  sub-directories of 1Mb or more:
    libs  66.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/egoTERGM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: 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

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  count_models_that_predict_synergies(...) not equal to 119.
  1/1 mismatches
  [1] 91 - 119 == -28
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
  1. Failure: it returns correct results (@test-analysis.R#8) 
  2. Failure: it returns correct results (@test-analysis.R#10) 
  3. Failure: it returns correct results (@test-analysis.R#11) 
  4. Failure: it returns correct results (@test-analysis.R#12) 
  5. Failure: it returns correct results (@test-analysis.R#14) 
  6. Failure: it returns correct results (@test-analysis.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   9.1Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.6Mb
Packages suggested but not available for checking: ‘xcms’ ‘MSnbase’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/eseis.Rcheck/00install.out’ for details.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ethnobotanyR.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/evclust.Rcheck/00install.out’ for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  19.2Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Undocumented code objects:
  ‘caption.etable’ ‘caption<-.etable’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Missing or unexported object: ‘optimx::hjn’
Running examples in ‘EZtune-Ex.R’ failed
The error most likely occurred in:

> ### Name: eztune
> ### Title: Supervised Learning Function
> ### Aliases: eztune
> 
> ### ** Examples
> 
> library(mlbench)
> data(Sonar)
> sonar <- Sonar[sample(1:nrow(Sonar), 100), ]
> 
> y <- sonar[, 61]
> x <- sonar[, 1:10]
> 
> # Optimize an SVM using the default fast setting and Hooke-Jeeves
> eztune(x, y)
Error: 'hjn' is not an exported object from 'namespace:optimx'
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 152-156 (EZtune.Rmd) 
Error: processing vignette 'EZtune.Rmd' failed with diagnostics:
'hjn' is not an exported object from 'namespace:optimx'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/factorial2x2.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FAMoS.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/FarmTest.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is 41.6Mb
  sub-directories of 1Mb or more:
    libs  41.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
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/fastR2.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.2Mb
Found the following significant warnings:
  Rconnection.cc:347:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  Rconnection.cc:356:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FastRWeb.Rcheck/00install.out’ for details.
Running ‘tinytest.R’ [55s/55s]
Running the tests in ‘tests/tinytest.R’ failed.
Last 13 lines of output:
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    0 tests    
  Running test_fastshap_titanic.R.......    1 tests [0;32mOK[0m 
  
  Running test_force_plot.R.............    0 tests    
  Exited 'test_force_plot.R' at lines 5-7. Skip force_plot tests for CRAN releases
  Error: ----- FAILED[data]: test_copy_classes.R<27--27>
   call| expect_identical(fastshap:::copy_classes(x, y), y)
   diff| Component "x3": 'is.NA' value mismatch: 2 in current 0 in target 
  In addition: There were 50 or more warnings (use warnings() to see the first 50)
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  33.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.9Mb
Packages required and available but unsuitable versions: ‘stats’ ‘utils’

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/fingerPro.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'set.seed(42, sample.kind = "Rounding")': unused argument (sample.kind = "Rounding") 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fingertipscharts.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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

Warning in normalizePath(f2) :
  path[1]="webshot65ceda5027d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot65ceda5027d.png': No such file or directory
Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.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 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.4Mb
Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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/fit4NM.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30480): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30485): 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
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30490): 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
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30495): 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
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30534): 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
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30539): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30544): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30549): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:30557): 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.
Running examples in ‘fit4NM-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit4NM
> ### Title: Platform for NONMEM
> ### Aliases: fit4NM
> ### Keywords: utilities
> 
> ### ** Examples
> 
> fit4NM()

(R:30576): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:30576): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:30576): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:30576): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:30576): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:30576): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:30576): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:30576): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:30576): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

 *** caught segfault ***
address 0x18, cause 'memory not mapped'

Traceback:
 1: .RGtkCall("S_gtk_widget_show", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: window$Show()
 4: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 5: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 6: gwindow("GUI for NONMEM", width = 850, height = 300)
 7: fit4NM()
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Package suggested but not available for checking: ‘devEMF’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/00install.out’ for details.
Package required but not available: ‘flowWorkspace’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FOCI.Rcheck/00install.out’ for details.
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
The following objects are masked from 'package:stats':

    filter, lag

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

    intersect, setdiff, setequal, union

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    margin

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

    combine

Quitting from lines 49-59 (custom_functions.Rmd) 
Error: processing vignette 'custom_functions.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/forestRK.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   4.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FrechForest.Rcheck/00install.out’ for details.
installed size is 56.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  55.2Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   5.7Mb
Packages suggested but not available for checking: ‘dggrids’ ‘INLA’
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  37.6Mb
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/fsbrain.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fullfact.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/fulltext.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FuzzyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.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/gainML.Rcheck/00install.out’ for details.
lms: no visible global function definition for ‘str2lang’
Undefined global functions or variables:
  str2lang
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.6Mb
installed size is 72.2Mb
  sub-directories of 1Mb or more:
    libs  71.8Mb
installed size is 53.6Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     50.4Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.9Mb
Error in re-building vignettes:
  ...
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
Execution halted
installed size is 143.8Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    140.2Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Package required but not available: ‘ShortRead’

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/GENEAsphere.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
S3 methods shown with full name in documentation object 'diseq':
  ‘diseq.ci’

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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GeNetIt.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
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/geoelectrics.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   3.6Mb
Running ‘testthat.R’ [18s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Must be a permutation of set {x,y,id,id.lengths,pathId,pathId.lengths,rule,name,gp,vp}
  
  Reading layer `nc' from data source `/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/sf/shape/nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 695 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 1 ]
  1. Failure: transform from geom to grob (@test_gc_grob.R#25) 
  
  Error: testthat unit tests failed
  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/geomorph.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GeoTcgaData.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
Running ‘testthat.R’ [35s/34s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: cache directory is created if necessary (@test_caching.R#29)  ───
  dir.exists(manage_cache$cache_path_get()) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 23 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: cache directory is created if necessary (@test_caching.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GFORCE.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
Execution halted
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ggenealogy.Rcheck/00install.out’ for details.
installed size is 20.2Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gggibbous.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 45-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:base':

    expand.grid

Loading required package: IRanges
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit


Attaching package: 'ape'

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

    complement

Quitting from lines 128-140 (ggmsa.Rmd) 
Error: processing vignette 'ggmsa.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-32 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   1.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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

Loading required package: Matrix
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 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x123629579
#1  0x123628945
#2  0x7fff93ac4529
sh: line 1: 96924 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/RtmpLCaVyQ/x1317a8c540f25fd/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  0x1235f6579
#1  0x1235f5945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.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
Package required and available but unsuitable version: ‘paletteer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 63.5Mb
  sub-directories of 1Mb or more:
    libs  62.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glmaag.Rcheck/00install.out’ for details.
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  58.5Mb
Found the following significant warnings:
  Note: possible error in 'glmnet(glmnet.data$x, ': unused argument (trace.it = trace.it) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glmnetcr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘glmnetcr-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.glmnetcr
> ### Title: Extract All Model Coefficients
> ### Aliases: coef.glmnetcr
> ### Keywords: methods
> 
> ### ** Examples
> 
> data(diabetes)
> x <- diabetes[, 2:dim(diabetes)[2]]
> y <- diabetes$y
> glmnet.fit <- glmnetcr(x, y)
Error in glmnet(glmnet.data$x, glmnet.data$y, family = "binomial", weights = glmnet.data$weights,  : 
  unused argument (trace.it = trace.it)
Calls: glmnetcr
Execution halted
Errors in running code in vignettes:
when running code in ‘glmnetcr.Rnw’
  ...

> x <- diabetes[, 2:dim(diabetes)[2]]

> y <- diabetes$y

> fit <- glmnetcr(x, y)

  When sourcing 'glmnetcr.R':
Error: unused argument (trace.it = trace.it)
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glmnet.Rcheck/00install.out’ for details.
Missing or unexported object: ‘glmnet::relax.glmnet’
Running examples in ‘glmnetUtils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cv.glmnet
> ### Title: Formula interface for elastic net cross-validation with
> ###   cv.glmnet
> ### Aliases: cv.glmnet cv.glmnet.default cv.glmnet.formula
> ###   predict.cv.glmnet.formula coef.cv.glmnet.formula
> ###   print.cv.glmnet.formula predict.cv.relaxed.formula
> ###   coef.cv.relaxed.formula
> 
> ### ** Examples
> 
> cv.glmnet(mpg ~ ., data=mtcars)
Error in glmnet(x, y, weights = weights, offset = offset, lambda = lambda,  : 
  unused arguments (gamma = gamma, relax = relax)
Calls: cv.glmnet -> cv.glmnet.formula -> <Anonymous>
Execution halted
Running ‘testthat.R’ [10s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Backtrace:
   1. glmnet::cv.glmnet(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 96 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 7 ]
  1. Error: (unknown) (@test2_cv_glmnet.R#11) 
  2. Error: mismatched factor levels work, cv.glmnet (@test4_predict.R#35) 
  3. Error: relaxed glmnet works (@test5_relaxed.R#7) 
  4. Error: relaxed glmnet works with weights and offset (@test5_relaxed.R#21) 
  5. Error: relaxed predict and coef work (@test5_relaxed.R#35) 
  6. Error: relaxed predict and coef work with nondefault gamma (@test5_relaxed.R#54) 
  7. Error: (unknown) (@test6_relaxed_cv.R#7) 
  
  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/glmpca.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Packages required but not available: ‘SeqArray’ ‘SeqVarTools’

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/gMOIP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer 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/gnmf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: possible error in 'RNGkind(sample.kind = "default")': unused argument (sample.kind = "default") 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gofCopula.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 33-34 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.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/GPareto.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.9Mb
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/GPoM.FDLyapu.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/GPoM.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 239-240 (gprofiler2.Rmd) 
Error: processing vignette 'gprofiler2.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  38.2Mb
Running ‘testthat.R’ [72s/79s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3096 | SKIPPED: 309 | WARNINGS: 0 | FAILED: 25 ]
  1. Error: gpuMatrix Double Precision Matrix-Vector multiplication (@test_gpuMatrix_algebra.R#840) 
  2. Error: gpuMatrix Integer Precision Sum (@test_gpuMatrix_row_col.R#41) 
  3. Error: gpuMatrix Double Precision Sum (@test_gpuMatrix_row_col.R#67) 
  4. Error: gpuMatrix Double Precision Block Sum (@test_gpuMatrix_row_col.R#400) 
  5. Error: gpuVector Double precision tcrossprod (@test_gpuVector_algebra.R#607) 
  6. Error: Switching GPUs vclMatrix Double Precision Matrix Multiplication (@test_switch_gpu_vclMatrix_algebra.R#480) 
  7. Error: Switching GPUs vclMatrix Double Precision Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#507) 
  8. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#535) 
  9. Error: Switching GPUs vclMatrix Double Precision Unary Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#567) 
  1. ...
  
  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/gRain.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘stats’ ‘grDevices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gratia.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘taxstats’ ‘taxstats1516’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gRbase.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gridGeometry.Rcheck/00install.out’ for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gsl.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 29372 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpjUDYzi/x13717e8f67458/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  0x121f26579
#1  0x121f25945
#2  0x7fff93ac4529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.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
Running ‘run-tests.R’ [2s/2s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  > f <- Filter(function(x) !grepl("html", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/gWidgets2/tests/button.R
  Loading required package: gWidgets2RGtk2
  Loading required package: memoise
  Loading required package: RGtk2
  No protocol specified
  R session is headless; GTK+ not initialized.
  Error in guiToolkit() : Can't load RGtk2
  Calls: sapply ... withVisible -> eval -> eval -> gwindow -> guiToolkit
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    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.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-107 (retype.Rmd) 
Error: processing vignette 'retype.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

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 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘glmnet’

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

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 1.0.0

Type citation('heatmaply') for how to cite the package.
Type ?heatmaply for the main documentation.

The github page is: https://github.com/talgalili/heatmaply/
Please submit your suggestions and bug-reports at: https://github.com/talgalili/heatmaply/issues
Or contact: <tal.galili@gmail.com>
======================

No protocol specified
Quitting from lines 108-110 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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 57-64 (geocoder.Rmd) 
Error: processing vignette 'geocoder.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  14.3Mb
Error in re-building vignettes:
  ...
Quitting from lines 434-443 (hetGP_vignette.Rnw) 
Error: processing vignette 'hetGP_vignette.Rnw' failed with diagnostics:
invalid 'z' limits
Execution halted
Package required but not available: ‘rtracklayer’

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/HierO.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.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use

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 52-53 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   1.2Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.9Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.1Mb
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/hmgm.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/hmmhdd.Rcheck/00install.out’ for details.
Package required but not available: ‘Rsamtools’

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.

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: lattice

Attaching package: 'mice'

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

    cbind, rbind

Quitting from lines 109-113 (simulating-data.Rmd) 
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘cairoDevice’ ‘RGtk2Extras’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hsstan.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Package suggested but not available for checking: ‘HTSFilter’
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hyper.fit.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hyperSpec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hypervolume.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IATscores.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...
Warning in engine$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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.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.
Welcome to DALEX (version: 0.4.7).
Find examples and detailed introduction at: https://pbiecek.github.io/PM_VEE/

randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
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]="webshot6a1c55d94b8c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot6a1c55d94b8c.png': No such file or directory
Quitting from lines 98-112 (vignette_iBreakDown_classification.Rmd) 
Error: processing vignette 'vignette_iBreakDown_classification.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘BSgenome’

Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.1000genomes.hs37d5’ ‘BSgenome.Hsapiens.UCSC.hg38’
  ‘BSgenome.Mmusculus.UCSC.mm10’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
Quitting from lines 84-88 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
argument of length 0
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   1.4Mb
    libs   5.1Mb
Package required but not available: ‘graphite’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Depends: includes the non-default packages:
  ‘lattice’ ‘caTools’ ‘gdata’ ‘gtools’ ‘gplots’ ‘parallel’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  58.6Mb
installed size is 28.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-104 (AplotIdiogramsVig.Rmd) 
Error: processing vignette 'AplotIdiogramsVig.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.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/igate.Rcheck/00install.out’ for details.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  14.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     17.1Mb
installed size is  8.3Mb
  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.
Quitting from lines 87-89 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
Execution halted
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: 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/Immigrate.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/impactflu.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   4.0Mb
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 29920 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2>/dev/null' had status 133
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  0x123592579
#1  0x123591945
#2  0x7fff93ac4529
Error: 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
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
Error in re-building vignettes:
  ...
Loading required package: 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

Loading required package: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Loading required package: gtools
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]="webshot10ff62900e600.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot10ff62900e600.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘GenomicAlignments’ ‘Rsamtools’ ‘apeglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Missing or unexported objects:
  ‘rhdf5::h5disableFileLocking’ ‘rhdf5::h5enableFileLocking’
  ‘rhdf5::h5testFileLocking’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Error in re-building vignettes:
  ...

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.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/irtplay.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.0Mb
Depends: includes the non-default packages:
  ‘partitions’ ‘VGAM’ ‘MASS’ ‘ape’ ‘apTreeshape’ ‘geiger’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/its.analysis.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘gurobi’ ‘cplexAPI’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ivmte.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/jackalope.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  # Percentage of value:     10.387%══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 60 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 13 ]
  1. Failure: Audit workflow (@test-auditPrior.R#44) 
  2. Failure: Evaluation with direct method (@test-evaluation.R#148) 
  3. Failure: Evaluation with direct method (@test-evaluation.R#149) 
  4. Failure: Evaluation with direct method (@test-evaluation.R#150) 
  5. Failure: Evaluation with difference method (@test-evaluation.R#160) 
  6. Failure: Evaluation with difference method (@test-evaluation.R#161) 
  7. Failure: Evaluation with difference method (@test-evaluation.R#162) 
  8. Failure: Evaluation with quotient method (@test-evaluation.R#172) 
  9. Failure: Evaluation with quotient method (@test-evaluation.R#173) 
  1. ...
  
  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/JFE.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/jomo.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.6Mb
Undocumented code objects:
  ‘tidy.glht’ ‘tidy.summary.glht’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  14.2Mb
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/KernSmoothIRT.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘FKF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/klustR.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/kmcudaR.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/knnp.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: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16

Quitting from lines 40-47 (hiv.Rmd) 
Error: processing vignette 'hiv.Rmd' failed with diagnostics:
cannot open the connection to 'http://hivdb.stanford.edu/pages/published_analysis/genophenoPNAS2006/DATA/PI_DATA.txt'
In addition: Warning messages:
1: In engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
2: In engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Packages suggested but not available for checking:
  ‘koRpus.lang.de’ ‘koRpus.lang.es’ ‘koRpus.lang.fr’ ‘koRpus.lang.it’
  ‘koRpus.lang.ru’

Package which this enhances but not available for checking: ‘rkward’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.9Mb
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.
Loading required package: ggplot2

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

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   7.2Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LambertW.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.7Mb
installed size is 120.6Mb
  sub-directories of 1Mb or more:
    libs  119.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/latticeExtra.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 139-237 (lbfgsb3c.Rmd) 
Error: processing vignette 'lbfgsb3c.Rmd' failed with diagnostics:
could not find function "opm"
Execution halted
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/lda.svi.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

trying URL 'https://raw.githubusercontent.com/emchristensen/Extreme-events-LDA/master/Rodent_table_dat.csv'
Content type 'text/plain; charset=utf-8' length 19291 bytes (18 KB)
==================================================
downloaded 18 KB

trying URL 'https://raw.githubusercontent.com/emchristensen/Extreme-events-LDA/master/LDA_figure_scripts.R'
Content type 'text/plain; charset=utf-8' length 11363 bytes (11 KB)
==================================================
downloaded 11 KB

trying URL 'https://raw.githubusercontent.com/weecology/PortalData/master/Rodents/moon_dates.csv'
Content type 'text/plain; charset=utf-8' length 15130 bytes (14 KB)
==================================================
downloaded 14 KB

trying URL 'https://raw.githubusercontent.com/weecology/PortalData/master/Rodents/Portal_rodent_trapping.csv'
Content type 'text/plain; charset=utf-8' length 272470 bytes (266 KB)
==================================================
downloaded 266 KB

Quitting from lines 169-187 (paper-comparison.Rmd) 
Error: processing vignette 'paper-comparison.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Package suggested but not available for checking: ‘rtracklayer’
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 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Problems with news in ‘inst/NEWS.Rd’:
  inst/NEWS.Rd:10: unknown macro '\proglang'
  inst/NEWS.Rd:47: unknown macro '\proglang'
  inst/NEWS.Rd:69: unknown macro '\proglang'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    extdata   1.1Mb
    libs      6.0Mb
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
Depends: includes the non-default packages:
  ‘sn’ ‘moments’ ‘BB’ ‘Bolstad2’ ‘optimx’ ‘Rmpfr’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in ‘LilRhino-Ex.R’ failed
The error most likely occurred in:

> ### Name: Random_Brains
> ### Title: Random Brains: Neural Network Implementation of Random Forest
> ### Aliases: Random_Brains
> 
> ### ** Examples
> 
> 
> dat = Cross_val_maker(iris, .2)
> 
> train = dat$Train
> test = dat$Test
> 
> Final_Test = Random_Brains(train[,-5],
+   train$Species, as.matrix(test[,-5]),
+   variables = 3, brains = 2)
Warning: Algorithm did not converge in 1 of 1 repetition(s) within the stepmax.
Error in cbind(1, pred) %*% weights[[num_hidden_layers + 1]] : 
  requires numeric/complex matrix/vector arguments
Calls: Random_Brains -> apply -> predict -> predict.nn
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.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 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
split_along_dim: no visible global function definition for ‘asplit’
Undefined global functions or variables:
  asplit
Running examples in ‘listarrays-Ex.R’ failed
The error most likely occurred in:

> ### Name: map_along_dim
> ### Title: Apply a function across subsets along an array dimension
> ### Aliases: map_along_dim map_along_rows map_along_cols
> 
> ### ** Examples
> 
> X <- matrix2(letters[1:15], ncol = 3)
> 
> apply(X, 1, function(x) paste(x, collapse = ""))   # simplifies to a vector
[1] "abc" "def" "ghi" "jkl" "mno"
> map_along_dim(X, 1, ~paste(.x, collapse = ""))     # returns a list
Error in asplit(as.array(X), which_dim) : 
  could not find function "asplit"
Calls: map_along_dim -> lapply -> split_along_dim
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. listarrays::split_along_rows(list(x1, x2, x3))
   2. listarrays::split_along_dim(X, 1L, depth = depth)
   3. base::lapply(...)
   4. listarrays:::FUN(X[[i]], ...)
   5. listarrays::split_along_dim(x, which_dim, depth = depth - 1L)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 74 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: specifying `which_dim` by name works (@test-dimnames.R#68) 
  2. Error: map_along_dim (@test-map.R#8) 
  3. Error: split_along_dim (@test-split.R#6) 
  4. Error: split* works recursively (@test-split.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.2Mb
    testdata   1.6Mb
Error in re-building vignettes:
  ...
Overfull \hbox (5.47499pt too wide) has occurred while \output is active
[] \T1/lmr/m/n/10.95 3
[3]

Package amsmath Warning: Foreign command \atop;
(amsmath)                \frac or \genfrac should be used instead
(amsmath)                 on input line 370.

! Undefined control sequence.
\c@lor@to@ps ->\PSTricks 
                         _Not_Configured_For_This_Format
l.370   \end
            {center}
? 
! Emergency stop.
\c@lor@to@ps ->\PSTricks 
                         _Not_Configured_For_This_Format
l.370   \end
            {center}
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on lmSubsets.log.
make: *** [all] Error 1
Error in buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/lmSubsets.Rcheck/vign_test/lmSubsets") : 
  running 'make' failed
Execution halted
Error in re-building vignettes:
  ...
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/loon.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 147 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#29) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘GeneticsPed’

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/LSAfun.Rcheck/00install.out’ for details.
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  47.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 63-64 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in mable(Vaal.Flow$Flow, M = c(2, 100), interval = c(0, 3000), IC = "all",  :
  The maximum candidate degree has been reached 
 with a p-value of the change-point 0.000000.
Warning in mable.ph(cbind(futime1, futime2) ~ age, data = ovarian2, M = c(2,  :
  
The maximum candidate degree has been reached 
with a p-value of the change-point 0.008885.
Warning in mable.ph(formula, data, M, g, pi0, tau, x0, controls, progress) :
  
The maximum candidate degree has been reached 
with a p-value of the change-point 0.008885.
Quitting from lines 370-372 (mable.Rmd) 
Error: processing vignette 'mable.Rmd' failed with diagnostics:
object 'Surv(Y, status)' not found
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MachineShop.Rcheck/00install.out’ for details.
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.6Mb
installed size is 78.9Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  71.6Mb
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  18.1Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2

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]="./webshot1b95497e3633.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1b95497e3633.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd023306255d6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd023306255d6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/maotai.Rcheck/00install.out’ for details.
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs         14.8Mb
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: raster
map images will be cached in  /tmp/RtmpJ9c2BX/mapmiscCache
Quitting from lines 221-238 (north.Rmd) 
Error: processing vignette 'north.Rmd' failed with diagnostics:
unable to find an inherited method for function 'coordinates' for signature '"numeric"'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 95-100 (intro.Rmd) 
Error: processing vignette 'intro.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/marindicators.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/markovchain.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   7.8Mb
Running ‘testthat.R’ [92s/92s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 2. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cas
  subscript out of bounds
  Backtrace:
   1. testthat::expect_equal(...)
   5. matrixTests::row_cosinor(x = x, t = numeric())
   7. base::`[<-.data.frame`(`*tmp*`, w2 | w3 | w6, c("f", "p"), value = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2096 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 2 ]
  1. Error: row eq col on 0 dimension matrix xs and ys (@test-col-versions.R#115) 
  2. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cases.R#82) 
  
  Error: testthat unit tests failed
  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/mcca.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.1Mb
surfacePlot : <anonymous>: no visible global function definition for
  ‘hcl.colors’
Undefined global functions or variables:
  hcl.colors
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MCMCpack.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
Depends: includes the non-default packages:
  ‘lattice’ ‘locfit’ ‘maptools’ ‘quantreg’ ‘RANN’ ‘SparseM’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
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/MDSMap.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/mdsOpt.Rcheck/00install.out’ for details.
installed size is 20.5Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
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.
Loading required package: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Loading required package: kinship2
Loading required package: quadprog
Loading required package: gdsfmt
Quitting from lines 694-696 (mega2rtutorial.Rmd) 
Error: processing vignette 'mega2rtutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.1Mb
installed size is 68.4Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Packages suggested but not available for checking: ‘clpAPI’ ‘ctc’
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 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/metamicrobiomeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...
    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


> library(HTSFilter)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘HTSFilter’
Execution halted
Error in re-building vignettes:
  ...
estimating dispersions
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
fitting model and testing
Loading required package: locfit
locfit 1.5-9.1 	 2013-03-22
Loading required package: lattice
    Welcome to 'DESeq'. For improved performance,
    usability and functionality, please consider
    migrating to 'DESeq2'.

Attaching package: ‘DESeq’

The following objects are masked from ‘package:DESeq2’:

    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 9 (label = DESeq1study) 
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
Execution halted
installed size is 69.4Mb
  sub-directories of 1Mb or more:
    libs  69.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   2.0Mb
    libs   2.3Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs  16.3Mb
    misc   1.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Package required and available but unsuitable version: ‘ECoL’

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: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.1Mb
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 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Running ‘testthat.R’ [51s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ...
  
  ── 2. Failure: (unknown) (@test-sampleMiceObj.R#22)  ───────────────────────────
  `moComp` not equal to `smComp`.
  Component "Dataset_1": Column 'Sepal.Length': 'is.NA' value mismatch: 15 in current 15 in target
  Component "Dataset_2": Column 'Sepal.Length': 'is.NA' value mismatch: 15 in current 15 in target
  Component "Dataset_3": Column 'Sepal.Length': 'is.NA' value mismatch: 15 in current 15 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: (unknown) (@test-sampleMiceObj.R#18) 
  2. Failure: (unknown) (@test-sampleMiceObj.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [19s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
Execution halted
Found the following significant warnings:
  Note: possible error in 'dev_package_deps(pkgdir = system.file(package = "microsamplingDesign"), ': unused argument (pkgdir = system.file(package = "microsamplingDesign")) 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/microsamplingDesign.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
runMicrosamplingDesignApp: possible error in dev_package_deps(pkgdir =
  system.file(package = "microsamplingDesign"), dependencies =
  "Suggests"): unused argument (pkgdir = system.file(package =
  "microsamplingDesign"))
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  21.8Mb
Package suggested but not available for checking: ‘glpkAPI’
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: Matrix
Loading required package: lattice
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'glpkAPI'
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.7Mb
Packages suggested but not available for checking: ‘mixAK’ ‘BRugs’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/missDeaths.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [41s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   iteration #: 21 
  
  
   Adjusting Variational EM for Stochastic Block Model
  
  	Imputation assumes a 'node' network-sampling process
  
   Initialization of model with 3 blocks. 
   Performing VEM inference for model with 3 blocks.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 458 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: miss SBM with covariates and node sampling works (@test-MISSSBM-fit-with-covariates.R#124) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’
Packages suggested but not available for checking:
  ‘minfi’ ‘IlluminaHumanMethylation450kmanifest’
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 png::readPNG(path, native = TRUE, info = TRUE) :
  libpng warning: iCCP: CRC error
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Depends: includes the non-default packages:
  ‘mlr3’ ‘mlr3db’ ‘mlr3filters’ ‘mlr3learners’ ‘mlr3pipelines’
  ‘mlr3tuning’ ‘mlr3viz’ ‘paradox’
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.
Quitting from lines 5-183 (./toc/vignettetoc.Rmd) 
Quitting from lines 5-183 (./toc/vignettetoc.Rmd) 
Error: processing vignette 'a_1_getting_started.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.7Mb
    libs   4.0Mb
Package required but not available: ‘clusterProfiler’

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/morphomap.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.5Mb
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.

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 342-344 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MPBoost.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mrfDepth.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 38.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  35.9Mb
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot3ae7a52012e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3ae7a52012e.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  15.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MTGS.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/MUACz.Rcheck/00install.out’ for details.
Packages required but not available: ‘org.Mm.eg.db’ ‘org.Ce.eg.db’

Package required and available but unsuitable version: ‘AnnotationDbi’

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

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/multigraph.Rcheck/00install.out’ for details.
installed size is 70.6Mb
  sub-directories of 1Mb or more:
    libs  70.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/multiplex.Rcheck/00install.out’ for details.
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x10f0c2c70, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  32: withOneRestart(expr, restarts[[1L]])
  33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  34: 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()    })
  35: FUN(X[[i]], ...)
  36: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  37: force(code)
  38: doWithOneRestart(return(expr), restart)
  39: withOneRestart(expr, restarts[[1L]])
  40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  41: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: 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)
  44: 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)
  45: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
Depends: includes the non-default packages:
  ‘car’ ‘pdist’ ‘pls’ ‘gplots’ ‘mvtnorm’ ‘robustbase’ ‘gtools’ ‘bitops’
  ‘caTools’ ‘pcaPP’ ‘rrcov’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
Package required but not available: ‘qpgraph’

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.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette_mvord.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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MXM.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
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/nat.nblast.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/nat.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/nat.templatebrains.Rcheck/00install.out’ for details.
Warning: declared S3 method 'plot3d.templatebrain' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
Running ‘testthat.R’ [101s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 131 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 36 ]
  1. Failure: linear regression (@test_forward_selection.R#15) 
  2. Failure: logistic regression (@test_forward_selection.R#31) 
  3. Failure: init.model (@test_forward_selection.R#43) 
  4. Failure: init.model (@test_forward_selection.R#45) 
  5. Failure: init.model (@test_forward_selection.R#54) 
  6. Failure: init.model (@test_forward_selection.R#56) 
  7. Failure: init.model (@test_forward_selection.R#61) 
  8. Failure: univariate filter (@test_forward_selection.R#101) 
  9. Failure: univariate filter (@test_forward_selection.R#111) 
  1. ...
  
  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/netjack.Rcheck/00install.out’ for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.6Mb
Packages suggested but not available for checking: ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

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

    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

Loading required package: graphite
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'graphite'
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
could not find function "pathways"
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/NGBVS.Rcheck/00install.out’ for details.
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.9Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          18.7Mb
    tests          1.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Ryacas

Attaching package: 'Ryacas'

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

    Simplify

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

    deriv

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

    %*%, I, determinant, diag, diag<-, lower.tri, upper.tri

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 404-495 (nlsr-devdoc.Rmd) 
Error: processing vignette 'nlsr-devdoc.Rmd' failed with diagnostics:
could not find function "optimr"
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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.
Error: processing vignette 'walkthrough.Rmd' failed with diagnostics:
(converted from warning) Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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/NNS.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/nonlinearTseries.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘lpSolve’ ‘gdata’ ‘Hmisc’ ‘rms’ ‘geometry’ ‘psych’ ‘pwt’
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.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd) 
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
Execution halted
Error in re-building vignettes:
  ...

    betweenness, bonpow, closeness, components, degree, dyad.census,
    evcent, hierarchy, is.connected, neighborhood, triad.census

Warning: Removed 3 rows containing missing values (geom_text).
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.
Starting the simulation
Initializing ... running ...
Time: 10 (10% of maximum length). Hosts count: 13 (6% of maximum infected hosts).
Time: 20 (20% of maximum length). Hosts count: 88 (44% of maximum infected hosts).
Time: 30 (30% of maximum length). Hosts count: 120 (60% of maximum infected hosts).
Time: 40 (40% of maximum length). Hosts count: 171 (86% of maximum infected hosts).
done. 
The simulation has run for 46 units of time and a total of 204 hosts have been infected.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 351-360 (output.Rmd) 
Error: processing vignette 'output.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/nsarfima.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/NTS.Rcheck/00install.out’ for details.
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  10.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
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/OceanView.Rcheck/00install.out’ for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.6Mb
    libs   2.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OCNet.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 35.1Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/onemap.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/OpenCL.Rcheck/00install.out’ for details.
installed size is 74.3Mb
  sub-directories of 1Mb or more:
    libs   64.6Mb
    share   9.7Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   5.9Mb
installed size is 172.0Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    161.9Mb
    models    4.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
Packages suggested but not available for checking:
  ‘gurobi’ ‘Rsymphony’ ‘lpsymphony’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘org.At.tair.db’
Running ‘bdstest.R’ [1s/1s]
  Running ‘hobbs.R’ [4s/5s]
Running the tests in ‘tests/hobbs.R’ failed.
Last 13 lines of output:
  In kktchk(ans$par, fn, wgr, hess = NULL, upper = NULL, lower = NULL,  :
    Eigenvalue failure for projected Hessian
  This problem is unconstrained.
  Error in lbfgsb3::lbfgsb3(prm = spar, fn = efn, gr = egr, control = mcontrol,  : 
    NA/NaN/Inf in foreign function call (arg 7)
  In addition: Warning messages:
  1: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  2: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  3: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  4: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  libc++abi.dylib: terminating with uncaught exception of type std::range_error: non-finite x values not allowed in calfun
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/optiSel.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.2Mb
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Package suggested but not available for checking: ‘IsoGene’
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/orthoDr.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ouch.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.
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 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
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.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘genbankr’

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

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

> ### Name: image_pal
> ### Title: Map data values to colours
> ### Aliases: image_pal image_raster image_stars
> 
> ### ** Examples
> 
> set.seed(28)
> vals <- sort(rnorm(100))
> cols <- image_pal(vals, zlim = c(-2.4, 2))
Error: 'hcl.colors' is not an exported object from 'namespace:grDevices'
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("palr")
  ── 1. Error: image pal (@test-basic.R#22)  ─────────────────────────────────────
  'hcl.colors' is not an exported object from 'namespace:grDevices'
  Backtrace:
    1. testthat::expect_length(image_pal(1:10), 10)
    4. palr::image_pal(1:10)
   10. grDevices::hcl.colors
   11. base::getExportedValue(pkg, name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 27 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: image pal (@test-basic.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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: sp
Quitting from lines 83-87 (palr.Rmd) 
Error: processing vignette 'palr.Rmd' failed with diagnostics:
'hcl.colors' is not an exported object from 'namespace:grDevices'
Execution halted
Undocumented code objects:
  ‘knit_print.summary.panel_data’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ 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.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.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/partitions.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 3. Failure: sim 4 produces same results as before (@test-simulation.R#26)  ──
  `sim4` not equal to `sim4_before`.
  Component "f_dv": Mean relative difference: 0.1759294
  Component "td_dv": Mean relative difference: 0.1087843
  Component "d_dv": Mean relative difference: 0.2325671
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 6 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 3 ]
  1. Failure: updt_winner_weights work if there are equal output
            activations (@test-helper_functions.R#19) 
  2. Failure: sim 1 produces same results as before (@test-simulation.R#11) 
  3. Failure: sim 4 produces same results as before (@test-simulation.R#26) 
  
  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/pathfindR.Rcheck/00install.out’ for details.
Package required but not available: ‘Mfuzz’

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/pbdMPI.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/pbdPROF.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/pca3d.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.5Mb
installed size is 96.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  93.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Failed with error:  'object 'as_data_frame' is not exported by 'namespace:tidytree''
Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PCRedux.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in st_centroid.sf(zones) :
  st_centroid assumes attributes are constant over geometries of x
Warning in st_centroid.sfc(st_geometry(x), of_largest_polygon = of_largest_polygon) :
  st_centroid does not give correct centroids for longitude/latitude data
Quitting from lines 109-116 (pct-international.Rmd) 
Error: processing vignette 'pct-international.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    libs    6.4Mb
    share  11.9Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/permGPU.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-59 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘PhenotypeSimulator.R’, ‘PhenotypeSimulator.Rmd’, ‘PhenotypeSimulator.html’, ‘PhenotypeSimulator.md’, ‘Sample-scripts-external-genotype-simulation.R’, ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘SimulationBasedOnExampleData.Rmd’, ‘Vignette-example-data.bib’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
Found the following significant warnings:
  phreeqcpp/transport.cpp:794:11: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phreeqc.Rcheck/00install.out’ for details.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot19c9635f8145.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19c9635f8145.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.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/phylocurve.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘graphics’ ‘grDevices’ ‘methods’ ‘stats’ ‘utils’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   8.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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]="webshot119101802bc3c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot119101802bc3c.png': No such file or directory
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
* installing *source* package ‘milne’ ...
** R
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (milne)

* installing *source* package ‘pkgnet’ ...
** package ‘pkgnet’ successfully unpacked and MD5 sums checked
** R
** inst
** byte-compile and prepare package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (pkgnet)
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 77-113 (pkgnet-intro.Rmd) 
Error: processing vignette 'pkgnet-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘rggobi’

Depends: includes the non-default packages:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘lattice’ ‘rggobi’ ‘ggplot2’
  ‘proto’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pksensi.Rcheck/00_pkg_src/pksensi/man/compile_model.Rd:16: unknown macro '\proglang'
  Warning: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pksensi.Rcheck/00_pkg_src/pksensi/man/compile_model.Rd:30: unknown macro '\proglang'
  Warning: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pksensi.Rcheck/00_pkg_src/pksensi/man/compile_model.Rd:34: unknown macro '\proglang'
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pksensi.Rcheck/00install.out’ for details.
aggregate.rankings: no visible global function definition for ‘asplit’
Undefined global functions or variables:
  asplit
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Packages required but not available:
  ‘VariantAnnotation’ ‘Rsamtools’ ‘rtracklayer’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
No protocol specified

(R:98062): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:98068): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:98074): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:98080): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:98097): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:98120): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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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:98125): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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(R:98131): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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(R:98136): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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(R:98145): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
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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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/plinkQC.Rcheck/00install.out’ for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.5Mb
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
1 samples were dropped from the abundance matrix for lack of associated covariates.
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.
corrplot 0.84 loaded

Attaching package: 'dplyr'

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

    combine

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning: Transformation introduced infinite values in continuous x-axis
Quitting from lines 186-190 (PLN.Rmd) 
Error: processing vignette 'PLN.Rmd' failed with diagnostics:
unused argument (options = options)
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/plotdap.Rcheck/00install.out’ for details.
raster_alpha: no visible global function definition for ‘asplit’
Undefined global functions or variables:
  asplit
Running examples in ‘plothelper-Ex.R’ failed
The error most likely occurred in:

> ### Name: raster_alpha
> ### Title: Combine a Matrix of Colors and a Matrix of Alpha Values
> ### Aliases: raster_alpha
> 
> ### ** Examples
> 
> # A color matrix
> co=c("red", "yellow", "green", "blue")
> co=rbind(co, co, co)
> # An alpha matrix
> alp=c(1, 0.6, 0.3, 0.1)
> alp=rbind(alp, alp, alp)
> # Now combine the two
> result=raster_alpha(co, alp)
Error in asplit(color, 2) : could not find function "asplit"
Calls: raster_alpha
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.8Mb
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.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 140-141 (vignette.Rmd) 
Error: processing vignette 'vignette.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/polyPK.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
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.

For example usage please run: vignette('qqman')

Citation appreciated but not required:
Turner, S.D. qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots. biorXiv DOI: 10.1101/005165 (2014).

Quitting from lines 410-413 (polyRADtutorial.Rmd) 
Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
there is no package called 'VariantAnnotation'
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

> suppressMessages(library(ROI.plugin.quadprog))

> suppressMessages(library(ROI.plugin.glpk))

  When sourcing ‘ROI_vignette.R’:
Error: there is no package called ‘ROI.plugin.glpk’
Execution halted
when running code in ‘portfolio_vignette.Rnw’
  ...

> maxret <- add.objective(portfolio = init, type = "return", 
+     name = "mean")

> opt_maxret <- optimize.portfolio(R = R, portfolio = maxret, 
+     optimize_method = "ROI", trace = TRUE)

  When sourcing ‘portfolio_vignette.R’:
Error: paste0("package:", plugin) %in% search() || requireNamespace(plugin,  .... is not TRUE
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'ROI_vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Running ‘test-all.R’ [3s/4s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  > #
  > # POUMM is distributed in the hope that it will be useful,
  > # but WITHOUT ANY WARRANTY; without even the implied warranty of
  > # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
  > # GNU General Public License for more details.
  > #
  > # You should have received a copy of the GNU General Public License
  > # along with POUMM  If not, see <http://www.gnu.org/licenses/>.
  > 
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
  libc++abi.dylib: terminating with uncaught exception of type Rcpp::exception: external pointer is not valid
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.
libc++abi.dylib: terminating with uncaught exception of type Rcpp::exception: external pointer is not valid
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PowerfulMaxEigenpair.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘tfse’

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/PPQplan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in normalizePath(f2) :
  path[1]="webshot14bcf369ecf62.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot14bcf369ecf62.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
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/predict3d.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: predict3d
No protocol specified
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Running ‘testthat.R’ [32s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [17] compiler_3.5.2     inum_1.0-1        
  > 
  > test_check("pre")
  ── 1. Failure: cvpre gives previous results with airquality data (@test_pre_misc
  `airq.cv.par` not equal to read_to_test("airquality_w_pre_cv_par").
  Component "accuracy": Component "MSE": Mean relative difference: 0.01912031
  Component "accuracy": Component "MAE": Mean relative difference: 0.0133677
  Component "cvpreds": Mean relative difference: 0.01639578
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 118 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: cvpre gives previous results with airquality data (@test_pre_misc.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/prioGene.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘gurobi’ ‘lpsymphony’ ‘Rsymphony’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   6.6Mb
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 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘prismatic-Ex.R’ failed
The error most likely occurred in:

> ### Name: clr_grayscale
> ### Title: Transform colors to greyscale
> ### Aliases: clr_grayscale clr_greyscale
> 
> ### ** Examples
> 
> 
> plot(clr_grayscale(rainbow(10)))
> 
> plot(clr_grayscale(terrain.colors(10)))
> 
> plot(clr_grayscale(hcl.colors(10), method = "luma"))
Error in hcl.colors(10) : could not find function "hcl.colors"
Calls: plot -> clr_grayscale -> color
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/probhat.Rcheck/00install.out’ for details.
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Error in re-building vignettes:
  ...

    intersect, setdiff, setequal, union

Loading required package: edeaR
Loading required package: eventdataR
Loading required package: processmapR
Loading required package: xesreadR
Loading required package: processmonitR
Loading required package: petrinetR

Attaching package: 'bupaR'

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

    filter

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

    timestamp

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 23-49 (use-external-data-to-change-tokens.Rmd) 
Error: processing vignette 'use-external-data-to-change-tokens.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.2Mb
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    1.4Mb
    libs   1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/psychonetrics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ptinpoly.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/pubh.Rcheck/00install.out’ for details.
installed size is 37.6Mb
  sub-directories of 1Mb or more:
    libs  37.3Mb
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Running ‘testthat.R’ [341s/243s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > testthat::test_check("pulsar")
  ── 1. Error: Job continues when subset of parallel jobs have errors/warnings (@t
  
  2 jobs failed with: "NA detected in data"
  Backtrace:
    1. testthat::expect_warning(...)
    9. pulsar::pulsar(...)
   10. pulsar:::.try_mclapply(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 315 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Job continues when subset of parallel jobs have errors/warnings (@test_errorreporting.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available:
  ‘Rsamtools’ ‘GenomicFeatures’ ‘GenomicAlignments’

Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’

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.
Quitting from lines 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 54.3Mb
  sub-directories of 1Mb or more:
    libs  54.1Mb
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/qpcR.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qtbase.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 20-35 (quadmesh.Rmd) 
Error: processing vignette 'quadmesh.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   9.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QZ.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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: ggplot2
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]="webshotaee2667e0478.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotaee2667e0478.png': No such file or directory
Quitting from lines 285-287 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘CoreGx’ ‘PharmacoGx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.5Mb
Package suggested but not available for checking: ‘CGHbase’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package unavailable to check Rd xrefs: ‘CGHbase’
Error in .requirePackage(package) : 
    unable to find required package 'CGHbase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  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/RAINBOWR.Rcheck/00install.out’ for details.
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    libs  30.0Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/randomizeR.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 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   8.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rarms.Rcheck/00install.out’ for details.
‘%<-%’
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Error in re-building vignettes:
  ...

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

    date

Loading required package: ggplot2

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

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   5.9Mb
Package required but not available: ‘Rirt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘rattle’
No protocol specified

(R:13664): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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/rayshader.Rcheck/00install.out’ for details.
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  30.1Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.3Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rchallenge)
  > 
  > test_check("rchallenge")
  ── 1. Failure: pandoc available (@test-pandoc.R#2)  ────────────────────────────
  rmarkdown::pandoc_available("1.12.3") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: pandoc available (@test-pandoc.R#2) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Depends: includes the non-default packages:
  ‘biclust’ ‘fabia’ ‘iBBiG’ ‘superbiclust’ ‘BcDiag’ ‘rqubic’ ‘BicARE’
  ‘s4vd’ ‘BiBitR’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rcplex.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    libs      1.9Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppMeCab.Rcheck/00install.out’ for details.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      24.0Mb
    libs      8.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.2Mb
    libs      4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcrypt.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 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.0Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rdist.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in normalizePath(f2) :
  path[1]="./webshot94d2112788b9.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot94d2112788b9.png': No such file or directory
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.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/rdtLite.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.4Mb
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 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    6.5Mb
    libs   2.4Mb
Error in re-building vignettes:
  ...

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

    show

Loading required package: ggplot2

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

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘plotdap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
S3 methods shown with full name in documentation object 'all.vars.character':
  ‘all.vars.character’

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.
Running ‘restfulr_unit_tests.R’ [3m/28m]
Running the tests in ‘tests/restfulr_unit_tests.R’ failed.
Last 13 lines of output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/.local/share/R/rsolr/solr-undertow-1.5.0-RC1-with-solr-5.3.0/lib/xnio-nio-3.4.0.Beta1.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
  WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  
  Execution halted
  rm: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprsxEQD: Too many open files
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/retistruct.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is 30.3Mb
  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/rfishnet2.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 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.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/RGCxGC.Rcheck/00install.out’ for details.
installed size is 121.2Mb
  sub-directories of 1Mb or more:
    libs      118.3Mb
    pictures    1.3Mb
Error in re-building vignettes:
  ...


Attaching package: 'lubridate'

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

    days, hours, minutes, seconds, years

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

    interval

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

    date

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]="webshot17496f892789.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17496f892789.png': No such file or directory
Quitting from lines 50-63 (precipitation_stochastic_generation_v6.Rmd) 
Error: processing vignette 'precipitation_stochastic_generation_v6.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
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
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMaCzek.Rcheck/00install.out’ for details.
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
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
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.4Mb
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/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
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.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.8Mb
installed size is 80.5Mb
  sub-directories of 1Mb or more:
    libs  79.9Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RRphylo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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: 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
No protocol specified

(R:80421): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:80424): 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:80427): 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:80430): 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:80445): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:80460): 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:80463): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:80466): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:80469): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:80475): 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.
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 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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
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/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmp24SaXC/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_29ad54f8df24/sourceCpp_2.so':
  dlopen(/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmp24SaXC/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_29ad54f8df24/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmp24SaXC/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_29ad54f8df24/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 10.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.8Mb
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.
Undocumented code objects:
  ‘type_sum.rxRateDur’
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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 11.3Mb
  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages which this enhances but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘pogs’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sclr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 14.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  11.3Mb
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/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
Packages suggested but not available for checking:
  ‘GenomicAlignments’ ‘muscle’ ‘Rsamtools’
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SeqNet.Rcheck/00install.out’ for details.
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 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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sglasso.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sgof.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SGPdata.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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 13-29 (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  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
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
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.3Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SmartEDA.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   8.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.2Mb
Error in re-building vignettes:
  ...
Warning in engine$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
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 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 ‘testsAtoC.R’ [22s/22s]
  Running ‘testsD.R’ [60s/60s]
Running the tests in ‘tests/testsD.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/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/spfrontier.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/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:44556): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:44565): 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:44575): 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:44583): 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:44605): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:44637): 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:44646): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:44654): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:44663): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:44675): 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:44692): 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’ [28s/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
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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
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:
  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
Package required but not available: ‘lpsymphony’

Packages suggested but not available for checking: ‘Rsymphony’ ‘gurobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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.
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.
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 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.
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]="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.
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’
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   3.7Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 65.0Mb
  sub-directories of 1Mb or more:
    libs  63.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WeibullFit.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
Package suggested but not available for checking: ‘org.Mm.eg.db’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/windAC.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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
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
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/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  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/44s]
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