Running ‘testthat.R’ [42s/42s]
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
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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
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 17.6Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.0Mb
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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  9.6Mb
  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs  35.1Mb
installed size is 44.1Mb
  sub-directories of 1Mb or more:
    libs  43.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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.
Running ‘test-all.R’ [33s/33s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Backtrace:
   1. rmarkdown::render(tf, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 961 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
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 70.2Mb
  sub-directories of 1Mb or more:
    libs  70.0Mb
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 0x102999c40, 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 ...
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
Running examples in ‘mvSLOUCH-Ex.R’ failed
The error most likely occurred in:

> ### Name: BrownianMotionModel
> ### Title: Estimate parameters under a Brownian motion model of evolution
> ### Aliases: BrownianMotionModel
> ### Keywords: models multivariate htest
> 
> ### ** Examples
> 
> RNGversion("3.6.1")
> set.seed(12345, kind = "Mersenne-Twister", normal.kind = "Inversion")
> ### We will first simulate a small phylogenetic tree  using functions from ape. 
> ### For simulating the tree one could also use alternative functions, eg. sim.bd.taxa 
> ### from the TreeSim package
> phyltree<-ape::rtree(5)
> 
> ## The line below is not necessary but advisable for speed
> phyltree<-phyltree_paths(phyltree)
> 
> ### Define Brownian motion parameters to be able to simulate data under 
> ### the Brownian motion model.
> BMparameters<-list(vX0=matrix(0,nrow=3,ncol=1),
+ Sxx=rbind(c(1,0,0),c(0.2,1,0),c(0.3,0.25,1)))
> 
> ### Now simulate the data.
> BMdata<-simulBMProcPhylTree(phyltree,X0=BMparameters$vX0,Sigma=BMparameters$Sxx)
> BMdata<-BMdata[phyltree$tip.label,,drop=FALSE]
> 
> ### Recover the parameters of the Brownian motion.
> BMestim<-BrownianMotionModel(phyltree,BMdata)
> 
> ### And finally obtain bootstrap condfidence intervals for some parameters
> BMbootstrap<-parametric.bootstrap(estimated.model=BMestim,phyltree=phyltree,
+ values.to.bootstrap=c("vX0","StS"),M.error=NULL,numboot=2)
Doing bootstrap iteration: 1. Start time: 2019-12-06 02:04:04
Doing bootstrap iteration: 2. Start time: 2019-12-06 02:04:04
> RNGversion(getRversion())
Error in strsplit(vstr, ".", fixed = TRUE) : non-character argument
Calls: RNGversion -> strsplit
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(temp_file_path)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
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.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’ [107s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 130 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 37 ]
  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#110) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   4.5Mb
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 35.8Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.8Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          18.7Mb
    tests          1.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/nlr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$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
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 18.3Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  10.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
Package required and available but unsuitable version: ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.6Mb
    libs   2.4Mb
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 35.0Mb
  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 171.9Mb
  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  9.1Mb
  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 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
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.
Warning 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 and available but unsuitable version: ‘groupedstats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Missing or unexported object: ‘grDevices::hcl.colors’
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
EAMM: no visible global function definition for ‘anova’
EAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘rand’
PAMM: no visible global function definition for ‘anova’
SSF: no visible global function definition for ‘rand’
SSF: no visible global function definition for ‘anova’
Undefined global functions or variables:
  anova rand
Consider adding
  importFrom("stats", "anova")
to your NAMESPACE file.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.1, GDAL 2.1.3, PROJ 4.9.3

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

Downloading constituency data
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]="webshot661c7d217110.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot661c7d217110.png': No such file or directory
Quitting from lines 65-110 (introduction.Rmd) 
Error: processing vignette 'introduction.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.
Packages required but not available: ‘pbdMPI’ ‘pbdSLAP’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

Package which this enhances but not available for checking: ‘pmclust’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’

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.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      1.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pcaL1.Rcheck/00install.out’ for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.5Mb
installed size is 88.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  85.2Mb
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Failed with error:  'object 'as_data_frame' is not exported by 'namespace:tidytree''
Quitting from lines 37-53 (PCMBase.Rmd) 
Error: processing vignette 'PCMBase.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PCRedux.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-59 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
Execution halted
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhaseType.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   3.1Mb
Error in re-building vignettes:
  ...
Warning in engine$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
Packages required and available but unsuitable versions:
  ‘graphics’ ‘grDevices’ ‘LINselect’ ‘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
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:97635): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:97640): 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:97645): 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:97650): 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:97667): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:97686): 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:97691): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:97696): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:97701): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:97709): 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.
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.
S3 methods shown with full name in documentation object 'rbind.fill':
  ‘rbind.fill’

S3 methods shown with full name in documentation object 'rbind.fill.matrix':
  ‘rbind.fill.matrix’

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   6.3Mb
    libs   1.9Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: GERMAPARLMINI
... activating corpus: REUTERS
Quitting from lines 139-140 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polyPK.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Error in re-building vignettes:
  ...
Warning in engine$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
Found the following significant warnings:
  whopgenome/whoptbi_info.cpp:116:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:122:7: 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]
  whopgenome/whoptbi_region.cpp:80:13: warning: 'this' pointer cannot be null 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/PopGenome.Rcheck/00install.out’ for details.
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
libc++abi.dylib: terminating with uncaught exception of type Rcpp::exception: external pointer is not valid
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PowerfulMaxEigenpair.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppcong.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PPQplan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$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’ [30s/36s]
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
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
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’
Running ‘testthat.R’ [75s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                                                            ^
  21 warnings generated.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 289 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 8 ]
  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) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘ALDEx2’
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.
Running ‘testthat.R’ [43s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    jurkat_06_100731121305
  Starting to work on MS/MS Peak shape ...
  
  Memory [MB] prior|after|max(diff) : 93.9 | 93.7 | 3969388 (3969294)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 119 | SKIPPED: 0 | WARNINGS: 128 | FAILED: 2 ]
  1. Failure: createReport (@test_computeQC.R#46) 
  2. Failure: createReport (@test_computeQC.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 33.8Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Running ‘testthat.R’ [337s/240s]
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
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/qMRI.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/qpcR.Rcheck/00install.out’ for details.
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.
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  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.3Mb
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
‘%<-%’
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’
Packages suggested but not available for checking:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2’
  ‘RGtk2Extras’
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
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  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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
Running ‘tests.R’ [8s/8s]
Running the tests in ‘tests/tests.R’ failed.
Last 13 lines of output:
  Backtrace:
    1. RDS::MA.estimates(...)
    2. RDS:::getnetest(...)
    3. RDS:::oneiteration(...)
    4. RDS:::fitnet.RDS(...)
   10. ergm:::InitErgmTerm.nodemix(...)
   11. ergm::check.ErgmTerm(...)
   12. ergm::ergm_Init_abort(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 24 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: rds-MA (@test-estimators.R#31) 
  
  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/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 19.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs  15.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.3Mb
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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rerddapXtracto.Rcheck/00install.out’ for details.
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/restatapi.Rcheck/00install.out’ for details.
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
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
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.

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
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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rirt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RISCA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rise.Rcheck/00install.out’ for details.
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  20.8Mb
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘golubEsets’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rLindo.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Error in re-building vignettes:
  ...
`type` used, `query` ignored.
Data retrieval 100%   
                                                                        
Found 12 interactions
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
Data retrieval 7.14%   
Data retrieval 14.3%   
Data retrieval 21.4%   
Data retrieval 28.6%   
Data retrieval 35.7%   
Data retrieval 42.9%   
Data retrieval 50%   
Data retrieval 57.1%   
Data retrieval 64.3%   
Data retrieval 71.4%   
Data retrieval 78.6%   
Data retrieval 85.7%   
Data retrieval 92.9%   
Data retrieval 100%   
                                                                        
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 251-258 (rmangal.Rmd) 
Error: processing vignette 'rmangal.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
installed size is 49.2Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  argument is of length zero
  Backtrace:
   1. testthat::expect_identical(...)
   4. rmdfiltr::add_lua_filter(...)
   5. rmdfiltr::add_custom_filter(...)
   6. rmdfiltr::verify_pandoc_version(report = report)
   7. utils::compareVersion("2.0", as.character(rmarkdown::pandoc_version()))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Convenience functions (@test_convenience_functions.R#4) 
  2. Error: Vectorization (@test_vectorization.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-45 (replace_ampersands.Rmd) 
Error: processing vignette 'replace_ampersands.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.4Mb
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.4Mb
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  25.5Mb
Running ‘testthat.R’ [108s/110s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("RMixtCompIO")
  ── 1. Failure: functional model works (@test.run.R#324)  ───────────────────────
  rand.index(partition, resGen$z) is not more than 0.9. Difference: -0.0646
  
          partition
  zPredict 1 2
         1 0 3
         2 3 0
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 39 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: functional model works (@test.run.R#324) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmpi.Rcheck/00install.out’ for details.
Packages required but not available: ‘Rata’ ‘Rirt’

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R       3.2Mb
    libs    2.0Mb
    tests   1.2Mb
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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.8Mb
installed size is 76.2Mb
  sub-directories of 1Mb or more:
    libs  75.6Mb
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  29.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

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

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor use Fortran I/O
nor system RNGs. The detected symbols are linked into the code but
might come from libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rsparse.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
installed size is 131.9Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     1.2Mb
    libs  128.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 2-15 (./children/SETTINGS-knitr.txt) 
Quitting from lines NA-15 (./children/SETTINGS-knitr.txt) 
Error: processing vignette 'aov.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 27.6Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 230.3Mb
  sub-directories of 1Mb or more:
    libs  227.6Mb
installed size is 63.6Mb
  sub-directories of 1Mb or more:
    libs  62.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  12.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rsymphony.Rcheck/00install.out’ for details.
Running ‘run_test.R’ [8s/8s]
Running the tests in ‘tests/run_test.R’ failed.
Complete output:
  > all_files <- list.files("testthat",full.names=T,pattern="*.R$")
  > 
  > sapply(all_files,source)
  Loading required package: magick
  Linking to ImageMagick 6.9.9.39
  Enabled features: cairo, fontconfig, freetype, lcms, pango, rsvg, webp
  Disabled features: fftw, ghostscript, x11
  Loading required package: XML
  Error: Test failed: 'RTestCollection write HTML summary errors'
  * `writeExecSummary.html(...)` produced warnings.
  * `writeExecSummary.html(...)` produced warnings.
  Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [6]  0.0394 -  0.0428 == -0.00345
  [7]  0.4000 -  0.0000 ==  0.40000
  [8]  0.6000 -  0.8000 == -0.20000
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 58 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
  1. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#36) 
  2. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#42) 
  3. Failure: transfer_entropy shannon is correctly specified (@test.transfer_entropy.R#77) 
  4. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#113) 
  5. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#119) 
  6. Failure: transfer_entropy renyi is correctly specified (@test.transfer_entropy.R#154) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot13a4b44c3aa91.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13a4b44c3aa91.png': No such file or directory
Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-26 (mcMat.Rmd) 
Error: processing vignette 'mcMat.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/Rtmpbd3Z4l/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_22ee40311ab4/sourceCpp_2.so':
  dlopen(/private/tmp/Rtmpbd3Z4l/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_22ee40311ab4/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/Rtmpbd3Z4l/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_22ee40311ab4/sourceCpp_2.so
  Reason: image not found
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   5.9Mb
Running ‘Arguments-FILES.R’ [0s/1s]
  Running ‘FileProgressBar.R’ [0s/0s]
Running the tests in ‘tests/FileProgressBar.R’ failed.
Last 13 lines of output:
  
  The following objects are masked from 'package:base':
  
      cat, commandArgs, getOption, inherits, isOpen, parse, warnings
  
  > 
  > # Creates a progress bar (of length 100) that displays it self as a file.
  > pb <- FileProgressBar("~/progress.simulation")
  Error in file(file, ifelse(append, "a", "w")) : 
    cannot open the connection
  Calls: FileProgressBar ... update.FileProgressBar -> cat -> cat.default -> <Anonymous> -> file
  In addition: Warning message:
  In file(file, ifelse(append, "a", "w")) :
    cannot open file '/Users/urbanek/progress.simulation': Read-only file system
  Execution halted
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs     57.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs    6.3Mb
    yacas   1.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs    7.0Mb
    yacas   1.3Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SafeBayes.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.4Mb
    libs   3.2Mb
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sclr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.8Mb
Running examples in ‘SDMtune-Ex.R’ failed
The error most likely occurred in:

> ### Name: aicc
> ### Title: AICc
> ### Aliases: aicc
> 
> ### ** Examples
> 
> # Acquire environmental variables
> files <- list.files(path = file.path(system.file(package = "dismo"), "ex"),
+                     pattern = "grd", full.names = TRUE)
> predictors <- raster::stack(files)
> 
> # Prepare presence and background locations
> p_coords <- virtualSp$presence
> bg_coords <- virtualSp$background
> 
> # Create SWD object
> data <- prepareSWD(species = "Virtual species", p = p_coords, a = bg_coords,
+                    env = predictors, categorical = "biome")
Extracting predictor information for presence locations...
Extracting predictor information for absence/background locations...
> 
> # Train a model
> model <- train(method = "Maxnet", data = data, fc = "l")
Error in get(fun, mode = "function", envir = parent.frame()) : 
  object 'trainMaxnet' of mode 'function' was not found
Calls: train -> do.call -> %in% -> formalArgs -> formals -> get
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [21s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("SDMtune")
  ── 1. Error: (unknown) (@test-utils.R#5)  ──────────────────────────────────────
  object 'trainANN' of mode 'function' was not found
  Backtrace:
   1. SDMtune::train("ANN", data = data, size = 10)
   4. methods::formalArgs(f)
   5. base::formals(def)
   6. base::get(fun, mode = "function", envir = parent.frame())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 353 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-utils.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   4.5Mb
Packages suggested but not available for checking: ‘flowMerge’ ‘flowClust’
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/semEff.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/semnar.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-50 (simulate_rnaseq.Rmd) 
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
there is no package called 'airway'
Execution halted
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   7.2Mb
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘SingleCellExperiment’ ‘MAST’ ‘rtracklayer’ ‘monocle’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 159.3Mb
  sub-directories of 1Mb or more:
    doc      12.0Mb
    libs    143.2Mb
    sqlite    1.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sglasso.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shapes.Rcheck/00install.out’ for details.
Depends: includes the non-default packages:
  ‘hdrcde’ ‘coda’ ‘MASS’ ‘bayesm’ ‘mnormt’ ‘spatstat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="webshot1057065329cc7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1057065329cc7.png': No such file or directory
Quitting from lines 28-44 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘maftools’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  10.8Mb
Package required but not available: ‘BSgenome’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  16.8Mb
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
Package required but not available: ‘rosr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sivipm.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  28.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SLEMI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 132-133 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   8.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.3Mb
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(sobir)
  > 
  > test_check("sobir")
  ── 1. Failure: perm_area should calculate the no-data zone areas for each permut
  bperm[7, 4] is not strictly less than 0.4. Difference: 0.0404
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 7 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: perm_area should calculate the no-data zone areas for each permutation of the data simulated nsim times (@tests.R#41) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotb6d773c33674.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb6d773c33674.png': No such file or directory
Quitting from lines 71-72 (understanding_sortable_js.Rmd) 
Error: processing vignette 'understanding_sortable_js.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Package unavailable to check Rd xrefs: ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.42 secs
Identifing all possible orderings..
Total run time: 0.88 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotaa8d67b04631.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotaa8d67b04631.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'RandomFields'

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

    RFoptions

Setting:
  options(
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
Paths set to:
  options(
    rasterTmpDir = '/private/tmp/RtmpA6jyhK/raster'
    reproducible.cachePath = '/private/tmp/RtmpA6jyhK/reproducible/cache'
    spades.inputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/inputs'
    spades.outputPath = '/private/tmp/RtmpPQP4Ao/SpaDES/outputs'
    spades.modulePath = '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SpaDES.core.Rcheck/SpaDES.core/sampleModules'
  )
simList saved in
 SpaDES.core:::.pkgEnv$.sim 
It will be deleted at next spades() call.
Quitting from lines 376-380 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  30.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.3Mb
Running examples in ‘spatialEco-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘raster’

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

    shift

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

 *** caught segfault ***
address 0x117f7fff8, cause 'memory not mapped'

Traceback:
 1: .terrain(as.double(values(x)), as.integer(dim(out)), rs, un,     nopt, lonlat, y)
 2: .local(x, ...)
 3: raster::terrain(elev, opt = c("slope", "aspect"), unit = "degrees")
 4: raster::terrain(elev, opt = c("slope", "aspect"), unit = "degrees")
An irrecoverable exception occurred. R is aborting now ...
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   9.4Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.8Mb
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
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/splithalfr.Rcheck/00install.out’ for details.
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:39597): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:39604): 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:39611): 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:39618): 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:39637): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:39660): 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:39667): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:39674): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:39681): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:39691): 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:39705): 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 ...
Packages required and available but unsuitable versions: ‘tergm’ ‘ergm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [63s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 270 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 53 ]
  1. Failure: t1way_ci works (@test-effsize_helpers.R#827) 
  2. Failure: t1way_ci works (@test-effsize_helpers.R#828) 
  3. Failure: t1way_ci works (@test-effsize_helpers.R#829) 
  4. Failure: t1way_ci works (@test-effsize_helpers.R#834) 
  5. Failure: t1way_ci works (@test-effsize_helpers.R#835) 
  6. Failure: t1way_ci works (@test-effsize_helpers.R#836) 
  7. Failure: t1way_ci works (@test-effsize_helpers.R#841) 
  8. Failure: t1way_ci works (@test-effsize_helpers.R#842) 
  9. Failure: t1way_ci works (@test-effsize_helpers.R#843) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘pvca’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/STGS.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SuppDists.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Surrogate.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  80.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Package suggested but not available for checking: ‘svHttp’
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Packages suggested but not available for checking: ‘sylly.de’ ‘sylly.es’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/symbolicDA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

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

> ### Name: tanaka
> ### Title: Plot a Tanaka Map
> ### Aliases: tanaka
> 
> ### ** Examples
> 
> library(tanaka)
> library(raster)
Loading required package: sp
> library(sf)
Linking to GEOS 3.7.2, GDAL 2.4.2, PROJ 5.2.0
> com <- st_read(system.file("gpkg/com.gpkg", package = "tanaka"),
+                quiet = TRUE)
> ras <- raster(system.file("grd/elev.grd", package = "tanaka"))
> tanaka(ras)
> tanaka(ras, mask = com)
> tanaka(ras, breaks = seq(80,400,20),
+        legend.pos = "topright",
+        legend.title = "Elevation\n(meters)")
> tanaka(ras, nclass = 15,
+        col = hcl.colors(15, "YlOrRd"),
+        legend.pos = "topright",
+        legend.title = "Elevation\n(meters)")
Error in hcl.colors(15, "YlOrRd") : could not find function "hcl.colors"
Calls: tanaka -> plot -> plot.sfc_MULTIPOLYGON
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 36.2Mb
  sub-directories of 1Mb or more:
    libs  34.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.4Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  14.8Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tensorsparse.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions: ‘ergm’ ‘MASS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Packages suggested but not available for checking:
  ‘lpsymphony’ ‘Rsymphony’ ‘gurobi’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 80-86 (slickr.Rmd) 
Error: processing vignette 'slickr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Running examples in ‘threejs-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphjs
> ### Title: Interactive 3D Graph Visualization
> ### Aliases: graphjs
> 
> ### ** Examples
> 
> set.seed(1)
> g <- sample_islands(3, 10, 5/10, 1)
> i <- cluster_optimal(g)
Error in cluster_optimal(g) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/thurstonianIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TideCurves.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (tidycwl.Rmd) 
Error: processing vignette 'tidycwl.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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

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’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘CoreGx’

Package suggested but not available for checking: ‘PharmacoGx’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TPMplt.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs      9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tree.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

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

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



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 137-139 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/trendsegmentR.Rcheck/00install.out’ for details.
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  72.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/trinROC.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 23, 2018 11:16:19 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:20 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
when running code in ‘GuideAppendix.Stex’
  ...

> options(continue = "  ")

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

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

  When sourcing ‘GuideAppendix.R’:
Error: Failed to connect to database: Error: Can't connect to local MySQL server through socket '/tmp/mysql.sock' (2)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TSdbi
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.util.Configuration init
INFO: No configuration found. Apply defaults.
Apr 23, 2018 11:16:26 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetDataStructure/QNA
Apr 23, 2018 11:16:28 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:29 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: https://stats.oecd.org/restsdmx/sdmx.ashx/GetData/QNA/CAN%2BUSA%2BMEX.B1_GE.CARSA.Q?format=compact_v2
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:30 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tsfknn.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: forecast
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot17f502de19e53.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17f502de19e53.png': No such file or directory
Quitting from lines 99-117 (TSplotly.Rmd) 
Error: processing vignette 'TSplotly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot1605266051148.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1605266051148.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TTAinterfaceTrendAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TukeyRegion.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘grDevices’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 195-196 (NCA.Rmd) 
Error: processing vignette 'NCA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 31.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       22.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

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]="webshot3fda3deb087e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3fda3deb087e.png': No such file or directory
Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: magic
Loading required package: abind

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


Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   5.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/UNPaC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/urlshorteneR.Rcheck/00install.out’ for details.
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
Packages suggested but not available for checking: ‘vaers’ ‘vaersND’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/vanddraabe.Rcheck/00install.out’ for details.
installed size is 120.8Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     119.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshoteaf72ee2e4d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshoteaf72ee2e4d.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/vcvComp.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      3.8Mb
    doc    1.2Mb
    help   2.9Mb
installed size is 54.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  53.3Mb
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘ggplot2’ in library.dynam(lib, package, package.lib):
 shared object ‘Rcpp.so’ not found
Execution halted
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  55.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WeibullFit.Rcheck/00install.out’ for details.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   1.5Mb
Package suggested but not available for checking: ‘org.Mm.eg.db’
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/windAC.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotdf9e332da123.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotdf9e332da123.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wtss.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
guardExecution: no visible binding for global variable ‘errorCondition’
guardExecution: no visible binding for global variable
  ‘warningCondition’
offensiveProgrammingWrapFunction: no visible global function definition
  for ‘str2lang’
opwf: no visible global function definition for ‘str2lang’
Undefined global functions or variables:
  errorCondition str2lang warningCondition
Running examples in ‘wyz.code.metaTesting-Ex.R’ failed
The error most likely occurred in:

> ### Name: generateData
> ### Title: Generate Data
> ### Aliases: generateData
> ### Keywords: programation utilities
> 
> ### ** Examples
> 
> # typical example
> op_sum <- opwf(sum, c('...', 'removeNA_b_1'))
Error in str2lang(bd) : could not find function "str2lang"
Calls: opwf
Execution halted
Running ‘testthat.R’ [8s/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
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/yarr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
package or namespace load failed for 'ggtree':
 object 'as_data_frame' is not exported by 'namespace:tidytree'
Execution halted
installed size is 34.4Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ZipRadius.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [27s/70s]
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