installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    include   5.7Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/home/ripley/R/packages/tests32/statnet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stellaRbase)
  > 
  > options(scipen = 25)
  > 
  > test_check("stellaRbase")
  ── 1. Failure: Row counts are correct. (@test-getEffects_Account.R#33)  ────────
  t2[["_embedded"]][["records"]] has length 3, not length 2.
  
  ── 2. Failure: Row counts are correct and consolidate between lists and data tab
  nrow(t8) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30)  ───
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 4. Failure: Row counts consolidate between lists and data tables. (@test-getP
  nrow(t6) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ── 5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 6. Failure: Row counts consolidate between lists and data tables. (@test-getT
  nrow(t7) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 208 SKIPPED: 0 FAILED: 6
  1. Failure: Row counts are correct. (@test-getEffects_Account.R#33) 
  2. Failure: Row counts are correct and consolidate between lists and data tables. (@test-getEffects_Account.R#52) 
  3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30) 
  4. Failure: Row counts consolidate between lists and data tables. (@test-getPayments_Account.R#39) 
  5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  6. Failure: Row counts consolidate between lists and data tables. (@test-getTransactions_Account.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R          2.2Mb
    datasets   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Building shared library for Rcpp code chunk...
make: Warning: Ignoring DistributedMake -j option
make: Warning: Ignoring DistributedMake -j option
make: Fatal error: Don't know how to make target `file61583be86066.o'
Current working directory /tmp/RtmpgMaaRW/sourceCpp-i386-pc-solaris2.10-0.12.17/sourcecpp_61587c9403d
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
`/home/ripley/R/gcc/etc/Makeconf' is up to date.
Quitting from lines 60-85 (strider.Rmd) 
Error: processing vignette 'strider.Rmd' failed with diagnostics:
Error occurred building shared library.
Execution halted
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.3Mb
Error in re-building vignettes:
  ...
Warning in engine$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 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
Execution halted
Package suggested but not available for checking: ‘phyloseq’
Error in .requirePackage(package) : 
    unable to find required package 'phyloseq'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/subprocess.Rcheck/00install.out’ for details.
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("moa/r_interface/OneStageClusterer", returnSig = "Lmoa/r_interface/RCompatibleDataStreamClusterer;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous>
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    doc    2.8Mb
    help   1.0Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
Running examples in ‘svd-Ex.R’ failed
The error most likely occurred in:

> ### Name: extmat
> ### Title: External matrices operations.
> ### Aliases: is.extmat extmat.ncol extmat.nrow extmat ematmul
> 
> ### ** Examples
> 
> ## Not run: 
> ##D library(Matrix)
> ##D f <- function(v) as.numeric(A %*% v) # Convert Matrix object back to vector
> ##D tf <- function(v) as.numeric(tA %*% v) # Convert Matrix object back to vector
> ##D 
> ##D e <- new.env()
> ##D assign("A", USCounties, e)
> ##D assign("tA", t(USCounties), e)
> ##D environment(f) <- e
> ##D environment(tf) <- e
> ##D 
> ##D m <-extmat(f, tf, nrow(USCounties), ncol(USCounties))
> ##D system.time(v1 <- propack.svd(m, neig = 10))
> ##D #   user  system elapsed 
> ##D #  0.252   0.007   0.259 
> ##D system.time(v2 <- propack.svd(as.matrix(USCounties), neig = 10))
> ##D #   user  system elapsed 
> ##D #  8.563   0.027   8.590 
> ## End(Not run)
> 
> # The largest eigenvalue and the corresponding eigenvector of a Hilbert matrix
> h <- outer(1:5000, 1:5000, function(i, j) 1 / (i + j - 1))
> v1 <- trlan.eigen(h, neig = 1)
> # Same, but using complex numbers
> v2 <- ztrlan.eigen(h, neig = 1)

 *** caught segfault ***
address 1f0, cause 'memory not mapped'

Traceback:
 1: ztrlan.eigen(h, neig = 1)
An irrecoverable exception occurred. R is aborting now ...
File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’

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

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

> ### Name: nullModel
> ### Title: SwapClass null model
> ### Aliases: nullModel
> 
> ### ** Examples
> 
> MAT=matrix(sample(0:3,50*20,replace=TRUE,prob=c(.7,.1,.1,.1)),ncol=20)
> 
> #Generation of null communities
> NULL_MATS=nullModel(MAT)

 *** caught segfault ***
address fd8105f0, cause 'memory not mapped'

Traceback:
 1: .Primitive(".C")(<pointer: fd8105f0>, mat0 = as.double(mat0),     mat = as.double(mat), nsim = as.integer(nsim), recursive = as.integer(recursive),     nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(Kb),     Kt = as.integer(Kt), strata = as.integer(strata), perms = as.double(perms))
 2: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 3: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 4: nullModel(MAT)
An irrecoverable exception occurred. R is aborting now ...
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: 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
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: -.tabplot
> ### Title: Compare two tableplots (experimental)
> ### Aliases: -.tabplot
> 
> ### ** Examples
> 
> # load diamonds dataset from ggplot2
> require(ggplot2)
Loading required package: ggplot2
> data(diamonds)
> 
> # calculate normalized prices to be used as sample probabilities
> price.norm <- with(diamonds, price / max(diamonds$price))
> 
> # draw samples
> exp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=price.norm, replace=TRUE),]
> chp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=1-price.norm, replace=TRUE),]
> 
> tp1 <- tableplot(exp.diamonds)
> tp2 <- tableplot(chp.diamonds)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  write error
Calls: tableplot ... clone.ffdf -> lapply -> FUN -> clone -> clone.ff -> assign -> ff
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    sql   8.9Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    3.9Mb
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/home/ripley/R/packages/tests32/tergm.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    4.1Mb
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: 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: nproc:  not found
Quitting from lines 111-113 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
Running examples in ‘TimeMachine-Ex.R’ failed
The error most likely occurred in:

> ### Name: mu.mle
> ### Title: Maximum-Likelihood Estimation of the Mutation Rate
> ### Aliases: mu.mle
> 
> ### ** Examples
> 
> # Load example dataset
> data(pdm)
> transitions <- full.transitions(pdm$unitary.transitions, pdm$loci)
> pi <- stationary.dist(transitions)
> 
> mu.int <- c(0.1, 10)
> samples <- 10
> 
> # MLE of the mutation rate for a single target population size
> n <- 10
> mle.res <- mu.mle(transitions, pi, pdm$population, n, mu.int, samples)
Error: C stack usage  189040340 is too close to the limit
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc         3.9Mb
    rmarkdown   1.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    3.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    doc    2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘phyloseq’

Package suggested but not available for checking: ‘adaptiveGPCA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
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 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/trialr.Rcheck/00install.out’ for details.
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  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: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc         5.5Mb
    dummydata   1.5Mb
    libs        1.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/unrtf.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
Running examples in ‘utiml-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctrl
> ### Title: CTRL model for multi-label Classification
> ### Aliases: ctrl
> 
> ### ** Examples
> 
> model <- ctrl(toyml, "RANDOM")
Error in ctrl(toyml, "RANDOM") : 
  There are no installed package 'FSelector' to use CTRL multi-label classifier
Execution halted
Running ‘testthat.R’ [21s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Error: CTRL (@test_brclassifiers.R#94)  ──────────────────────────────────
  There are no installed package 'FSelector' to use CTRL multi-label classifier
  1: ctrl(train, "RANDOM") at testthat/test_brclassifiers.R:94
  2: stop(paste("There are no installed package 'FSelector' to use CTRL", "multi-label classifier"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1120 SKIPPED: 21 FAILED: 1
  1. Error: CTRL (@test_brclassifiers.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
File ‘uuid/libs/uuid.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 123-126 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.3Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           5.7Mb
    htmlwidgets   4.6Mb
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 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 12.2Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 112: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
File ‘waffect/libs/waffect.so’:
  Found ‘rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   3.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.5Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 218-220 (wflow-01-getting-started.Rmd) 
Error: processing vignette 'wflow-01-getting-started.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Package required but not available: ‘x12’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/x12.Rcheck/00install.out’ for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    exampleData   1.5Mb
    examples      4.6Mb
Running examples in ‘XRJulia-Ex.R’ failed
The error most likely occurred in:

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found
Error in base::system(cmd, intern = TRUE) : 
  error in running command: 'Illegal seek'
Calls: findJulia -> testJSON -> <Anonymous>
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.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/zstdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > library(bagRboostR)
  > 
  > test_package("bagRboostR")
  ── 1. Error: samme returns a character vector of predicted classes (@test_samme.
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Running ‘testthat.R’ [3s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(biolink)
  > 
  > test_check("biolink")
  ── 1. Error: Reference KEGG Pathway URL is valid (@test-links-kegg.r#7)  ───────
  GnuTLS recv error (-110): The TLS connection was non-properly terminated.
  1: expect_equal(check_url_status(url), 200) at testthat/test-links-kegg.r:7
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: check_url_status(url)
  5: httr::GET(url) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/biolink.Rcheck/tests/testthat/helper-functions.r:4
  6: request_perform(req, hu$handle$handle)
  7: request_fetch(req$output, req$url, handle)
  8: request_fetch.write_memory(req$output, req$url, handle)
  9: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 103 SKIPPED: 7 FAILED: 1
  1. Error: Reference KEGG Pathway URL is valid (@test-links-kegg.r#7) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘blkergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘blkergm’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/blkergm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Boom.Rcheck/00install.out’ for details.
package ‘Boom’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
package ‘Boom’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Missing link or links in documentation object 'add.dynamic.regression.Rd':
  ‘SdPrior’

Missing link or links in documentation object 'plot.bsts.mixed.Rd':
  ‘TimeSeriesBoxplot’

See section 'Cross-references' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘btergm’
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘btergm’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/btergm.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7f9651caf820, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Running examples in ‘CANSIM2R-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getCANSIM
> ### Title: getCANSIM
> ### Aliases: getCANSIM
> 
> ### ** Examples
> 
> getCANSIM(4010004, showLabels = FALSE)
Warning in open.connection(file, "rt") :
  cannot open zip file '/tmp/RtmprjcETt/filec951b9f24f7'
Error in open.connection(file, "rt") : cannot open the connection
Calls: getCANSIM ... downloadCANSIM -> read.csv -> read.table -> open -> open.connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/cstab.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: Removed 92 rows containing missing values (geom_path).
Warning: Removed 71 rows containing missing values (geom_path).
Warning: Removed 120 rows containing missing values (geom_path).
Warning: Removed 125 rows containing missing values (geom_path).
Warning: Removed 30 rows containing missing values (geom_path).
Jun 18, 2018 7:53:54 PM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemBLAS
Jun 18, 2018 7:53:54 PM com.github.fommil.netlib.BLAS <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefBLAS
Jun 18, 2018 7:53:54 PM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemLAPACK
Jun 18, 2018 7:53:54 PM com.github.fommil.netlib.LAPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefLAPACK
Killed
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  ── 1. Error: returns normal (@test-earth.R#5)  ─────────────────────────────────
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.759,-125.673&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
  1: expect_is(get_earthtones(), "palette") at testthat/test-earth.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: get_earthtones()
  5: ggmap::get_map(location = c(longitude, latitude), maptype = "satellite", zoom = zoom, 
         ...)
  6: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging, 
         urlonly = urlonly, force = force, filename = filename, color = color, language = language)
  7: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: returns normal (@test-earth.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.count’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.count’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ergm.count.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘ergm.ego’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘ergm.ego’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ergm.ego.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.graphlets’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.graphlets’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ergm.graphlets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.rank’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.rank’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ergm.rank.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘ergm.userterms’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘ergm.userterms’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ergm.userterms.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [6s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ess)
  > 
  > test_check("ess")
  ── 1. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Italy") not equal to c(1, 2, 6).
  Lengths differ: 4 is not 3
  
  ── 2. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Spain") not equal to 1:7.
  Lengths differ: 8 is not 7
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 23 FAILED: 2
  1. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#100) 
  2. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
    user system elapsed
fcr 8.38   0.41  10.922
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of ‘|’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gRbase.Rcheck/00install.out’ for details.
Running ‘run-tests.R’ [2s/4s]
Running the tests in ‘tests/run-tests.R’ failed.
Complete output:
  > library(testthat)
  > library(gWidgets2)
  Loading required package: digest
  > options(guiToolkit="tcltk")
  > 
  > f <- list.files(system.file("tests", package="gWidgets2"), full=T)
  > f <- Filter(function(x) !grepl("README", x), f)
  > f <- Filter(function(x) !grepl("html", x), f)
  > ## issues
  > f <- Filter(function(x) !grepl("df.R", x), f)
  > f <- Filter(function(x) !grepl("text.R", x), f)
  > f <- Filter(function(x) !grepl("tree.R", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gWidgets2/tests/button.R
  Loading required package: gWidgets2tcltk
  Loading required package: memoise
  Loading required package: tcltk
  testing /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gWidgets2/tests/calendar.R
  testing /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gWidgets2/tests/checkbox.R
  testing /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gWidgets2/tests/combobox.R
  testing /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/gWidgets2/tests/containers.R
  Error: svalue(cards) not equal to 1.
  Modes: logical, numeric
  target is logical, current is numeric
  Execution halted
Running examples in ‘imfr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: imf_codes
> ### Title: Retrieve individual database codes
> ### Aliases: imf_codes
> 
> ### ** Examples
> 
> # Retrieve indicators from BOP database
> test = imf_codes(codelist = 'CL_INDICATOR_BOP')

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Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 223-235 (acf.Rmd) 
Error: processing vignette ‘acf.Rmd’ failed with diagnostics:
Different lengths of x and y.
Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘ergm::colMeans.mcmc.list’ by ‘statnet.common::colMeans.mcmc.list’ when loading ‘latentnet’
  Warning: replacing previous import ‘ergm::sweep.mcmc.list’ by ‘statnet.common::sweep.mcmc.list’ when loading ‘latentnet’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/latentnet.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.4657.
trying URL ‘http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz’
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
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downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.5287.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Killed
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ModelMetrics.Rcheck/00install.out’ for details.
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/4s]
  Running ‘testthat.R’ [20s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ── 1. Error: Bigglm distances (@test.match_on.R#298)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.match_on.R:298
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ── 2. Error: scores with bigglm (@test.scores.R#222)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.scores.R:222
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1308 SKIPPED: 0 FAILED: 2
  1. Error: Bigglm distances (@test.match_on.R#298) 
  2. Error: scores with bigglm (@test.scores.R#222) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 126-132 (Maps_and_Timeseries_Plots.Rmd) 
Error: processing vignette ‘Maps_and_Timeseries_Plots.Rmd’ failed with diagnostics:
cannot open URL ‘http://maps.google.com/maps/api/staticmap?center=47,-118&zoom=7&size=640x640&maptype=roadmap&format=png32&sensor=true’
Execution halted
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: estfun.Rchoice
> ### Title: Gradient for observations
> ### Aliases: estfun.Rchoice
> 
> ### ** Examples
> 
> ## Probit model
> data("Workmroz")
> probit <- Rchoice(lfp ~ k5 + k618 + age + wc + hc + lwg + inc,  
+                   data = Workmroz , family = binomial('probit'))
> summary(probit)

Model: binomial
Model estimated on: Mon Jun 18 06:16:20 PM 2018 

Call:
Rchoice(formula = lfp ~ k5 + k618 + age + wc + hc + lwg + inc, 
    data = Workmroz, family = binomial("probit"), method = "nr")


Frequencies of categories:
y
     0      1 
0.4316 0.5684 
The estimation took: 0h:0m:0s 

Coefficients:
          Estimate Std. Error z-value Pr(>|z|)    
constant  1.918422   0.380654   5.040 4.66e-07 ***
k5       -0.874711   0.113558  -7.703 1.33e-14 ***
k618     -0.038594   0.040489  -0.953 0.340488    
age      -0.037824   0.007609  -4.971 6.67e-07 ***
wc        0.488314   0.135487   3.604 0.000313 ***
hc        0.057170   0.124005   0.461 0.644776    
lwg       0.365629   0.087779   4.165 3.11e-05 ***
inc      -0.020525   0.004777  -4.297 1.73e-05 ***
---
Signif. codes:  0 ‘***’ 0.001 ‘**’ 0.01 ‘*’ 0.05 ‘.’ 0.1 ‘ ’ 1

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Found the following significant warnings:
  atkClasses.c:1050:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1058:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1397:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1948:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1964:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8665:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11110:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RGtk2.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’
File ‘rJava/libs/rJava.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Killed
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  newmat5.cpp:525:69: warning: throw will always call terminate() [-Wterminate]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmixmod.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [3s/145s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  ── 1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  ──────────────
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [5s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-src_translate_env.R#52)  ----------------------
  translate_sql(as(x, 0), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DOUBLE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS \"DOUBLE\")"
  
  -- 2. Failure: as() works (@test-src_translate_env.R#56)  ----------------------
  translate_sql(pmax(x), con = conn[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-src_translate_env.R#60)  ----------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS \"ARRAY<VARCHAR>\")").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS \"ARRAY<VARCHAR>\")"
  
  -- 4. Failure: as() works (@test-src_translate_env.R#69)  ----------------------
  translate_sql_(list(substituted.expression), con = conn[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS \"DATE\")").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-06-18')"
  y[1]: "CAST(\"x\" AS \"DATE\")"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 223 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-src_translate_env.R#52) 
  2. Failure: as() works (@test-src_translate_env.R#56) 
  3. Failure: as() works (@test-src_translate_env.R#60) 
  4. Failure: as() works (@test-src_translate_env.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RRF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/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’
File ‘Rserve/libs/Rserve.so’:
  Found no calls to: ‘R_registerRoutines’, ‘R_useDynamicSymbols’

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.
It is good practice to register native routines and to disable symbol
search.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  bitmap.c:1594:29: warning: suggest parentheses around comparison in operand of ‘^’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rttf2pt1.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SpaDES.core.Rcheck/00install.out’ for details.
Found the following significant warnings:
  wdl.cpp:184:7: warning: suggest parentheses around comparison in operand of ‘&’ [-Wparentheses]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘statnet’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘statnet’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/statnet.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [7s/37s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stellaRbase)
  > 
  > options(scipen = 25)
  > 
  > test_check("stellaRbase")
  ── 1. Failure: Row counts are correct. (@test-getEffects_Account.R#33)  ────────
  t2[["_embedded"]][["records"]] has length 3, not length 2.
  
  ── 2. Failure: Row counts are correct and consolidate between lists and data tab
  nrow(t8) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  ── 3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30)  ───
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 4. Failure: Row counts consolidate between lists and data tables. (@test-getP
  nrow(t6) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ── 5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  ── 6. Failure: Row counts consolidate between lists and data tables. (@test-getT
  nrow(t7) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 208 SKIPPED: 0 FAILED: 6
  1. Failure: Row counts are correct. (@test-getEffects_Account.R#33) 
  2. Failure: Row counts are correct and consolidate between lists and data tables. (@test-getEffects_Account.R#52) 
  3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30) 
  4. Failure: Row counts consolidate between lists and data tables. (@test-getPayments_Account.R#39) 
  5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  6. Failure: Row counts consolidate between lists and data tables. (@test-getTransactions_Account.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: replacing previous import ‘statnet.common::colMeans.mcmc.list’ by ‘ergm::colMeans.mcmc.list’ when loading ‘tergm’
  Warning: replacing previous import ‘statnet.common::sweep.mcmc.list’ by ‘ergm::sweep.mcmc.list’ when loading ‘tergm’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/tergm.Rcheck/00install.out’ for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
'library' or 'require' calls in package code:
  'MASS' 'Matrix'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
IIR: no visible global function definition for 'qnorm'
TIR: no visible global function definition for 'qnorm'
agreement: no visible global function definition for 'var'
agreement: no visible global function definition for 'pchisq'
agreement: no visible global function definition for 'dnorm'
agreement: no visible global function definition for 'qnorm'
html.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'plot'
plot.report: no visible global function definition for 'axis'
plot.report: no visible global function definition for 'points'
unified.agreement: no visible global function definition for 'lm'
unified.agreement: no visible global function definition for 'qnorm'
unified.agreement: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AnthropMMD.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.1Mb
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-06-17 23:03:29] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... github2versions -> getURL -> curlPerform -> <Anonymous> -> fun
Execution halted
plot.BIPOD: no visible global function definition for 'par'
plot.BIPOD: no visible global function definition for 'matplot'
plot.BIPOD: no visible global function definition for 'abline'
plot.BIPOD: no visible global function definition for 'plot'
plot.BIPOD: no visible global function definition for 'density'
plot.BIPOD: no visible global function definition for 'curve'
plot.BIPOD: no visible global function definition for 'dlnorm'
plot.BIPOD: no visible global function definition for 'dnorm'
plot.BIPOD: no visible global function definition for 'acf'
plot.BIPOD: no visible global function definition for 'pairs'
plot.BIPOD : standfun: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'sd'
plot.BIPOD: no visible global function definition for 'points'
plot.BIPOD: no visible global function definition for 'tail'
plot.BIPOD: no visible global function definition for 'matlines'
plot.BIPOD: no visible binding for global variable 'quantile'
plot.BIPOD: no visible global function definition for 'lines'
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'blkergm'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'blkergm'
See 'd:/Rcompile/CRANpkg/local/3.5/blkergm.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BonEV.Rcheck/00install.out' for details.
print.boolprob: no visible global function definition for 'plot'
print.boolprof: no visible global function definition for 'plot'
start_msg: no visible global function definition for
  'packageDescription'
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'btergm'
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'btergm'
See 'd:/Rcompile/CRANpkg/local/3.5/btergm.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
plot.CellularAutomaton: no visible global function definition for
  'image'
Undefined global functions or variables:
  image
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
Found the following hidden files and directories:
  .project
These were most likely included in error. See section 'Package
structure' in the 'Writing R Extensions' manual.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for 'gen.beta'
plotCVcggd: no visible binding for global variable 'cv'
plotCVcggd: no visible binding for global variable 'cv.error'
predict.cggd: no visible binding for global variable 'max.tk'
predict.cggd: no visible global function definition for 'gen.beta'
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
S3 methods shown with full name in documentation object 'plot.cggd':
  'plot.cggd'

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.
CGH.fused.lasso.one.fast: no visible global function definition for
  'lowess'
L2L1ExpandFit: no visible global function definition for
  'L2L1PathExtract'
consensusFDR: no visible global function definition for 'pbinom'
my.mad: no visible global function definition for 'median'
output.cghFLasso: no visible global function definition for
  'write.table'
plot.CGH.FL.All: no visible global function definition for 'plot'
plot.CGH.FL.All: no visible global function definition for 'segments'
plot.CGH.FL.All: no visible global function definition for 'text'
plot.CGH.FL.Consensus: no visible global function definition for
  'rainbow'
plot.CGH.FL.Consensus: no visible global function definition for 'plot'
plot.CGH.FL.Consensus: no visible global function definition for
  'segments'
plot.CGH.FL.Consensus: no visible global function definition for 'gray'
plot.CGH.FL.Consensus: no visible global function definition for 'text'
plot.CGH.FL.Single: no visible global function definition for 'plot'
plot.CGH.FL.Single: no visible global function definition for 'gray'
plot.CGH.FL.Single: no visible global function definition for
  'segments'
plot.CGH.FL.Single: no visible global function definition for 'text'
plot.cghFLasso: no visible global function definition for 'plot'
plot.cghFLasso: no visible global function definition for 'gray'
plot.cghFLasso: no visible global function definition for 'abline'
plot.cghFLasso: no visible global function definition for 'points'
segment.score: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  L2L1PathExtract abline gray lowess median pbinom plot pnorm points
  rainbow segments text write.table
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "abline", "plot", "points", "segments", "text")
  importFrom("stats", "lowess", "median", "pbinom", "pnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.cghFLasso':
  'plot.cghFLasso'

S3 methods shown with full name in documentation object 'summary.cghFLasso':
  'summary.cghFLasso' 'print.summary.cghFLasso'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Running 'test-all.R' [28s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(cli)
  > library(testthat)
  > old.env <- Sys.getenv("checkpoint.mock.install")
  > Sys.setenv("checkpoint.mock.install" = TRUE)
  > test_check("checkpoint")
  Loading required package: checkpoint
  
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/CircStats.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
cv.clogitL1 : <anonymous>: no visible global function definition for
  'var'
plot.clogitL1: no visible global function definition for 'matplot'
plot.clogitL1: no visible global function definition for 'legend'
plot.clogitL1: no visible global function definition for 'text'
plot.cv.clogitL1: no visible global function definition for 'matplot'
plot.cv.clogitL1: no visible global function definition for 'matlines'
plot.cv.clogitL1: no visible global function definition for 'points'
plot.cv.clogitL1: no visible global function definition for 'axis'
plot.cv.clogitL1: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis legend matlines matplot points text var
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "matlines",
             "matplot", "points", "text")
  importFrom("stats", "var")
to your NAMESPACE file.
find.antimodeMLE: no visible global function definition for 'par'
find.decreasingMLE: no visible global function definition for 'chull'
find.decreasingMLE: no visible global function definition for 'points'
find.increasingMLE: no visible global function definition for 'chull'
find.increasingMLE: no visible global function definition for 'points'
find.modeMLE: no visible global function definition for 'par'
plot.CPHshape: no visible global function definition for 'plot'
plot.CPHshape: no visible global function definition for 'segments'
plot.CPHshape: no visible global function definition for 'abline'
plot.CPHshape: no visible global function definition for 'grey'
plot.CPHshape: no visible global function definition for 'points'
Undefined global functions or variables:
  abline chull grey par plot points segments
Consider adding
  importFrom("grDevices", "chull", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
D.SN: no visible global function definition for 'dnorm'
D.SN: no visible global function definition for 'pnorm'
beta2cp: no visible global function definition for 'pnorm'
cSFM.est: no visible global function definition for 'optim'
cSFM.est: no visible global function definition for 'qnorm'
cSFM.est: no visible global function definition for 'cor'
case2.b.initial: no visible global function definition for 'var'
case2.gr: no visible global function definition for 'pnorm'
case2.gr: no visible global function definition for 'dnorm'
case2.unmll.optim: no visible global function definition for 'pnorm'
cp2beta: no visible global function definition for 'qnorm'
data.generator.y.F: no visible global function definition for 'cov2cor'
data.generator.y.F: no visible global function definition for 'rnorm'
data.generator.y.F : <anonymous>: no visible global function definition
  for 'pnorm'
g: no visible global function definition for 'dnorm'
g: no visible global function definition for 'pnorm'
predict.cSFM : <anonymous>: no visible global function definition for
  'qnorm'
predict.cSFM: no visible global function definition for 'qnorm'
predict.cSFM: no visible global function definition for 'pnorm'
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "qnorm", "rnorm", "var")
to your NAMESPACE file.
Found the following significant warnings:
  instabCorrection.cpp:34:10: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/cstab.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cudaBayesreg.Rcheck/00install.out' for details.
'library' or 'require' call to 'locfit' which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'R.methodsS3' 'R.oo' 'locfit' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
curvefit: no visible global function definition for 'model.frame'
curvefit: no visible global function definition for 'model.response'
curvefit: no visible global function definition for 'model.matrix'
curvetest: no visible global function definition for 'model.frame'
curvetest: no visible global function definition for 'plot'
curvetest.raw: no visible global function definition for 'pt'
curvetest.raw: no visible global function definition for 'pnorm'
getoptimalalpha: no visible global function definition for 'gcvplot'
getoptimalalpha: no visible global function definition for 'plot'
lines.curvefit: no visible global function definition for 'lines'
plot.curvefit: no visible global function definition for 'plot'
plot.curvefit: no visible global function definition for 'lines'
plot.curvefit: no visible global function definition for 'points'
Undefined global functions or variables:
  gcvplot lines model.frame model.matrix model.response plot pnorm
  points pt
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pnorm", "pt")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.7Mb
Running 'has-devel.R' [3s]
  Running 'test-that.R' [103s]
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/diffusionMap.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Curvature: no visible global function definition for 'tail'
gen.rarefac.div: no visible global function definition for 'sd'
plot.fitsingleMod: no visible global function definition for 'points'
plot.fitsingleMod: no visible global function definition for 'lines'
ref.area: no visible global function definition for 'integrate'
simm: no visible global function definition for 'integrate'
Undefined global functions or variables:
  integrate lines points sd tail
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "integrate", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  'FKF' 'dlm'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'dlm::dlmSmooth.dlmFiltered'
dlmodeler.extract: no visible global function definition for 'qnorm'
dlmodeler.fit.MAD: no visible global function definition for 'optim'
dlmodeler.fit.MAPE: no visible global function definition for 'optim'
dlmodeler.fit.MLE: no visible global function definition for 'optim'
dlmodeler.fit.MSE: no visible global function definition for 'optim'
dlmodeler.fit.sigma : fit.fun: no visible global function definition
  for 'var'
dlmodeler.fit.sigma: no visible global function definition for 'optim'
dlmodeler.forecast: no visible global function definition for 'qnorm'
Undefined global functions or variables:
  optim qnorm var
Consider adding
  importFrom("stats", "optim", "qnorm", "var")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/dpcR.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
dsCHECK: no visible global function definition for 'na.omit'
dsFC: no visible global function definition for 'cor'
dsMC: no visible global function definition for 'cor'
plot.ds: no visible global function definition for 'plot'
plot.ds: no visible global function definition for 'par'
plot.ds: no visible global function definition for 'points'
plot.ds: no visible global function definition for 'text'
Undefined global functions or variables:
  cor na.omit par plot points text
Consider adding
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "cor", "na.omit")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs   3.9Mb
elmtrain.default: no visible global function definition for 'runif'
elmtrain.formula: no visible global function definition for
  'model.frame'
elmtrain.formula: no visible global function definition for
  'model.matrix'
elmtrain.formula: no visible global function definition for
  'model.response'
predict.elmNN: no visible global function definition for 'fitted'
predict.elmNN: no visible global function definition for 'model.matrix'
print.elmNN: no visible global function definition for 'head'
print.elmNN: no visible global function definition for 'fitted'
randomMatrix: no visible global function definition for 'runif'
Undefined global functions or variables:
  fitted head model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "fitted", "model.frame", "model.matrix",
             "model.response", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
elrm: no visible global function definition for 'write.table'
plot.elrm: no visible global function definition for 'dev.new'
progress: no visible global function definition for 'flush.console'
update.elrm: no visible global function definition for 'write.table'
Undefined global functions or variables:
  dev.new flush.console write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File 'elrm/libs/i386/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'
File 'elrm/libs/x64/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/EnvStats.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.count'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.count'
See 'd:/Rcompile/CRANpkg/local/3.5/ergm.count.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'ergm::colMeans.mcmc.list' by 'statnet.common::colMeans.mcmc.list' when loading 'ergm.ego'
  Warning: replacing previous import 'ergm::sweep.mcmc.list' by 'statnet.common::sweep.mcmc.list' when loading 'ergm.ego'
See 'd:/Rcompile/CRANpkg/local/3.5/ergm.ego.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.graphlets'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.graphlets'
See 'd:/Rcompile/CRANpkg/local/3.5/ergm.graphlets.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.rank'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.rank'
See 'd:/Rcompile/CRANpkg/local/3.5/ergm.rank.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.userterms'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.userterms'
See 'd:/Rcompile/CRANpkg/local/3.5/ergm.userterms.Rcheck/00install.out' for details.
Running 'testthat.R' [27s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ess)
  > 
  > test_check("ess")
  -- 1. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Italy") not equal to c(1, 2, 6).
  Lengths differ: 4 is not 3
  
  -- 2. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Spain") not equal to 1:7.
  Lengths differ: 8 is not 7
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 23 FAILED: 2
  1. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#100) 
  2. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  'lars' 'ncvreg'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.path: no visible global function definition for 'par'
plot.path: no visible global function definition for 'plot'
plot.path: no visible global function definition for 'axis'
plot.path: no visible global function definition for 'points'
plot.path: no visible global function definition for 'abline'
Undefined global functions or variables:
  abline axis par plot points
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "points")
to your NAMESPACE file.
countBamInGRanges.exomeDepth: no visible global function definition for
  'as'
Undefined global functions or variables:
  as
Consider adding
  importFrom("methods", "as")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpsD0I3Y\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\Rtmpe6vUcq\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
plot.cf: no visible global function definition for 'barplot'
plot.cf: no visible global function definition for 'lines'
plot.cf: no visible global function definition for 'abline'
plot.cf: no visible global function definition for 'axis'
plot.cf: no visible global function definition for 'curve'
plot.tvm: no visible global function definition for 'barplot'
plot.tvm: no visible global function definition for 'lines'
tvm: no visible global function definition for 'uniroot'
update.tvm: no visible global function definition for 'uniroot'
Undefined global functions or variables:
  abline axis barplot curve lines uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "curve", "lines")
  importFrom("stats", "uniroot")
to your NAMESPACE file.
FlimFormula: no visible global function definition for 'is'
FlimFormula: no visible global function definition for 'terms'
FlimFormula: no visible global function definition for 'reformulate'
ImputateMissingValues : RegFun: no visible global function definition
  for 'lm'
ImputateMissingValues : RegFun: no visible binding for global variable
  'na.omit'
ImputateMissingValues: no visible global function definition for
  'predict'
ImputateMissingValues: no visible global function definition for
  'model.matrix'
ImputateMissingValues: no visible global function definition for 'coef'
flimList: no visible global function definition for 'coef'
flimSD: no visible binding for global variable 'sd'
plot.flim: no visible global function definition for 'plot'
plot.flim: no visible global function definition for 'lines'
plot.flim: no visible global function definition for 'points'
plot.flimList: no visible global function definition for 'par'
plot.flimList: no visible global function definition for 'plot'
plot.flimboot: no visible global function definition for 'plot'
plot.flimboot: no visible global function definition for 'points'
plot.flimboot: no visible global function definition for 'lines'
spaplot: no visible global function definition for 'plot'
spaplot: no visible global function definition for 'lines'
Undefined global functions or variables:
  coef is lines lm model.matrix na.omit par plot points predict
  reformulate sd terms
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "coef", "lm", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/fpc.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  -- 1. Failure: Catch unit tests pass (@test-cpp.R#5)  --------------------------
  C++ unit tests:
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   is a Catch v1.9.6 host application.
  Run with -? for options
  
  -------------------------------------------------------------------------------
  Entropy tests | test-cpp.cpp
    Numeric entropy - comparsion with entropy package
  -------------------------------------------------------------------------------
  test-cpp.cpp:26
  ...............................................................................
  
  test-cpp.cpp:33: FAILED:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
GAPerm : pmxCrossover: no visible global function definition for
  'runif'
GAReal : twoPointsCrossover: no visible global function definition for
  'runif'
GAReal : blendCrossover: no visible global function definition for
  'runif'
GAReal : mutateNoise: no visible global function definition for 'runif'
GAReal : initPopulation: no visible global function definition for
  'runif'
plot.GAPerm: no visible global function definition for 'plot'
plot.GAPerm: no visible global function definition for 'grid'
plot.GAPerm: no visible global function definition for 'lines'
plot.GAPerm: no visible global function definition for 'legend'
plot.GAReal: no visible global function definition for 'plot'
plot.GAReal: no visible global function definition for 'grid'
plot.GAReal: no visible global function definition for 'lines'
plot.GAReal: no visible global function definition for 'legend'
Undefined global functions or variables:
  grid legend lines plot runif
Consider adding
  importFrom("graphics", "grid", "legend", "lines", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gpuR.Rcheck/00install.out' for details.
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    R  19.2Mb
Package in Depends field not imported from: 'dismo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  _t_array_properties.cpp:10:13: warning: suggest parentheses around comparison in operand of '|' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/gRbase.Rcheck/00install.out' for details.
Package required but not available: 'EnsDb.Rnorvegicus.v79'

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

> ### Name: unByteCode
> ### Title: Convert a Byte-Code Function to an Interpreted-Code Function
> ### Aliases: unByteCode unByteCodeAssign assignEdgewise
> ### Keywords: programming utilites
> 
> ### ** Examples
> 
> datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
> dat <- as.matrix(read.csv(file=datURL, row.names=1))
Warning in file(file, "rt") :
  cannot open URL 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659': HTTP status was '500 Internal Server Error'
Error in file(file, "rt") : cannot open the connection
Calls: as.matrix -> read.csv -> read.table -> file
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

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

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Running examples in 'gutenbergr-Ex.R' failed
The error most likely occurred in:

> ### Name: gutenberg_strip
> ### Title: Strip header and footer content from a Project Gutenberg book
> ### Aliases: gutenberg_strip
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> book <- gutenberg_works(title == "Pride and Prejudice") %>%
+   gutenberg_download(strip = FALSE)
Determining mirror for Project Gutenberg from http://www.gutenberg.org/robot/harvest
Error in open.connection(con, "rb") : HTTP error 403.
Calls: %>% ... structure -> read_connection -> open -> open.connection
Execution halted
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(gutenbergr)
  > 
  > test_check("gutenbergr")
  -- 1. Error: gutenberg_get_mirror works (@test-download.R#8)  ------------------
  HTTP error 403.
  1: gutenberg_get_mirror() at testthat/test-download.R:8
  2: readr::read_lines(wget_url)
  3: datasource(file, skip = skip)
  4: datasource_connection(file, skip, comment)
  5: datasource_raw(read_connection(path), skip, comment = comment)
  6: new_datasource("raw", text, skip = skip, comment = comment)
  7: structure(list(x, skip = skip, comment = comment, ...), class = c(paste0("source_", 
         type), "source"))
  8: read_connection(path)
  9: open(con, "rb")
  10: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 44 SKIPPED: 1 FAILED: 1
  1. Error: gutenberg_get_mirror works (@test-download.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 136.4Mb
  sub-directories of 1Mb or more:
    java  134.7Mb
haplo.ccs: no visible global function definition for 'terms'
haplo.ccs: no visible global function definition for 'model.response'
haplo.ccs: no visible global function definition for 'model.matrix'
haplo.ccs.fit: no visible global function definition for 'glm'
haplo.ccs.fit: no visible global function definition for
  'quasibinomial'
haplo.ccs.fit: no visible binding for global variable 'logit'
haplo.ccs.fit: no visible global function definition for 'coef'
print.summary.haplo.ccs: no visible global function definition for 'pt'
sandcov: no visible global function definition for 'coef'
sandcov: no visible global function definition for 'model.matrix'
sandcov: no visible global function definition for 'residuals'
Undefined global functions or variables:
  coef glm logit model.matrix model.response pt quasibinomial residuals
  terms
Consider adding
  importFrom("stats", "coef", "glm", "model.matrix", "model.response",
             "pt", "quasibinomial", "residuals", "terms")
to your NAMESPACE file.
plot.threshpt: no visible global function definition for 'glm'
plot.threshpt: no visible global function definition for 'predict'
plot.threshpt: no visible global function definition for 'plot'
plot.threshpt: no visible global function definition for 'lines'
plot.threshpt: no visible global function definition for 'abline'
plot.threshpt: no visible global function definition for 'points'
print.summary.threshpt: no visible global function definition for
  'printCoefmat'
threshpt: no visible global function definition for 'as.formula'
threshpt: no visible global function definition for 'glm'
threshpt: no visible global function definition for 'vcov'
threshpt: no visible global function definition for 'pnorm'
threshpt: no visible global function definition for 'predict'
Undefined global functions or variables:
  abline as.formula glm lines plot pnorm points predict printCoefmat
  vcov
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "as.formula", "glm", "pnorm", "predict",
             "printCoefmat", "vcov")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/htmlwidgets.Rcheck/00install.out' for details.
ConfigureIBHM : <anonymous>: no visible global function definition for
  'dnorm'
FindActiv: no visible global function definition for 'sd'
OptimizeActivCMAES: no visible global function definition for 'runif'
OptimizeActivNM: no visible global function definition for 'optim'
OptimizeActivNM: no visible global function definition for 'runif'
OptimizeAllParams : goal: no visible global function definition for
  'relist'
OptimizeAllParams: no visible global function definition for 'optim'
OptimizeAllParams: no visible global function definition for 'relist'
OptimizeAllWeights: no visible global function definition for 'optim'
OptimizeScalCMAES: no visible global function definition for 'runif'
OptimizeScalNM: no visible global function definition for 'optim'
OptimizeScalNM: no visible global function definition for 'runif'
OptimizeWeights: no visible global function definition for 'optim'
TrainIBHM: no visible global function definition for 'enableJIT'
ValidationSC : <anonymous>: no visible global function definition for
  'predict'
group.by.samplesPerDim: no visible global function definition for 'sd'
summary.IBHM: no visible global function definition for 'predict'
summary.IBHM: no visible global function definition for 'sd'
summary.IBHM: no visible global function definition for 'cor'
Undefined global functions or variables:
  cor dnorm enableJIT optim predict relist runif sd
Consider adding
  importFrom("stats", "cor", "dnorm", "optim", "predict", "runif", "sd")
  importFrom("utils", "relist")
to your NAMESPACE file.
'library' or 'require' call to 'tcltk' which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: 'tcltk'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpsB20PK\ex_data2ea245a9b4c97.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpsB20PK\ex_data2ea245a9b4c97.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
.iabline.AB: no visible global function definition for 'coefficients'
.iobj.opt.PlotPolygon: no visible global function definition for
  'xy.coords'
.ivar.check.length: no visible global function definition for
  'flush.console'
ilines: no visible global function definition for 'xy.coords'
iplot: no visible global function definition for 'xy.coords'
itext: no visible global function definition for 'xy.coords'
Undefined global functions or variables:
  coefficients flush.console xy.coords
Consider adding
  importFrom("grDevices", "xy.coords")
  importFrom("stats", "coefficients")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'MASS' 'nlme' 'survival'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
JointRegBC.default : f: no visible global function definition for
  'pnorm'
JointRegBC.default : f: no visible global function definition for
  'dnorm'
JointRegBC.default: no visible global function definition for 'nlminb'
JointRegBC.default: no visible global function definition for 'fdHess'
JointRegBC.default: no visible global function definition for 'ginv'
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
CoxFit : GetEstimate: no visible global function definition for 'lm'
CoxFit : GetEstimate: no visible global function definition for 'vcov'
CoxModel_Year: no visible global function definition for 'model.frame'
CoxModel_Year: no visible global function definition for 'model.matrix'
joinpoint: no visible global function definition for 'as.formula'
joinpoint: no visible global function definition for 'model.frame'
joinpoint: no visible global function definition for 'model.matrix'
joinpoint : plot.surv: no visible global function definition for
  'predict'
joinpoint : plot.surv: no visible global function definition for 'plot'
joinpoint : plot.surv: no visible global function definition for
  'lines'
joinpoint : plot.surv: no visible global function definition for
  'legend'
read.seerstat: no visible global function definition for 'read.table'
Undefined global functions or variables:
  as.formula legend lines lm model.frame model.matrix plot predict
  read.table vcov
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "lm", "model.frame", "model.matrix",
             "predict", "vcov")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> result = knockoff.filter(X, y, knockoffs=knockoffs,
+                            statistic=stat.stability_selection)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 89 99
> 
> # Advanced usage with custom arguments
> foo = stat.stability_selection
> k_stat = function(X, X_k, y) foo(X, X_k, y, fitfun=stabs::lars.lasso)
> result = knockoff.filter(X, y, knockoffs=knockoffs, statistic=k_stat)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 65 89 99
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  43.23 1.32 43.89 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(kofdata)
  Loading required package: jsonlite
  Loading required package: httr
  > 
  > test_check("kofdata")
  -- 1. Failure: get_metadata works (@test_get_metadata.R#5)  --------------------
  is.na(get_metadata("ch.kof.bau.run1.ng08.f12.q_cb_restrict_none.ans_count.d11")) isn't false.
  
  == testthat results  ===========================================================
  OK: 25 SKIPPED: 0 FAILED: 1
  1. Failure: get_metadata works (@test_get_metadata.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
Found the following significant warnings:
  Warning: replacing previous import 'ergm::colMeans.mcmc.list' by 'statnet.common::colMeans.mcmc.list' when loading 'latentnet'
  Warning: replacing previous import 'ergm::sweep.mcmc.list' by 'statnet.common::sweep.mcmc.list' when loading 'latentnet'
See 'd:/Rcompile/CRANpkg/local/3.5/latentnet.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
LICurvature.default : f: no visible global function definition for
  'dnorm'
LICurvature.default: no visible global function definition for 'nlminb'
LICurvature.default: no visible global function definition for 'ginv'
Undefined global functions or variables:
  dnorm ginv nlminb
Consider adding
  importFrom("stats", "dnorm", "nlminb")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   1.6Mb
LVMMCOR.default : f: no visible global function definition for 'pnorm'
LVMMCOR.default : f: no visible global function definition for 'dnorm'
LVMMCOR.default: no visible global function definition for 'nlminb'
LVMMCOR.default: no visible global function definition for 'fdHess'
LVMMCOR.default: no visible global function definition for 'ginv'
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/maGUI.Rcheck/00install.out' for details.
plot.mathgraph: no visible global function definition for 'plot'
plot.mathgraph: no visible global function definition for 'box'
plot.mathgraph: no visible global function definition for 'segments'
plot.mathgraph: no visible global function definition for 'arrows'
plot.mathgraph: no visible global function definition for 'text'
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
find.cb : plotit: no visible global function definition for 'plot'
find.cb : plotit: no visible global function definition for 'points'
find.cb : plotit: no visible global function definition for 'title'
plot.MCbound: no visible global function definition for 'par'
plot.MCbound: no visible global function definition for 'plot'
plot.MCbound: no visible global function definition for 'lines'
plot.MCbound: no visible global function definition for 'points'
plot.MCbound: no visible global function definition for 'axis'
plot.MCbound: no visible global function definition for 'mtext'
Undefined global functions or variables:
  axis lines mtext par plot points title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot",
             "points", "title")
to your NAMESPACE file.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
mdr.3WS: no visible global function definition for 'combn'
mdr.cv: no visible global function definition for 'combn'
permute.mdr : mdr.lrt: no visible global function definition for
  'combn'
permute.mdr : mdr.lrt: no visible global function definition for 'glm'
permute.mdr : mdr.lrt: no visible global function definition for
  'as.formula'
permute.mdr : mdr.lrt: no visible global function definition for
  'binomial'
permute.mdr : mdr.lrt: no visible binding for global variable 'logit'
plot.mdr: no visible global function definition for 'formula'
Undefined global functions or variables:
  as.formula binomial combn formula glm logit
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MetaIntegrator.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MM2S.Rcheck/00install.out' for details.
'library' or 'require' calls in package code:
  'MASS' 'parallel'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  confusionMatrix_.cpp:10:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:12:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:14:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:16:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:57:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:104:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:106:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:108:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
  confusionMatrix_.cpp:110:29: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/ModelMetrics.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/MSeasy.Rcheck/00install.out' for details.
'library' or 'require' call to 'igraph' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'Rcpp'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File 'NetSim/libs/i386/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'
File 'NetSim/libs/x64/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         6.5Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/npde.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
    libs   1.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     5.9Mb
    models   4.6Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Ord.logreg: no visible binding for global variable 'data'
plot.Ord.logreg: no visible global function definition for 'par'
plot.Ord.logreg: no visible global function definition for 'plot'
plot.Ord.logreg: no visible global function definition for 'mtext'
plot.Ord.logreg: no visible global function definition for 'plot.new'
Undefined global functions or variables:
  data mtext par plot plot.new
Consider adding
  importFrom("graphics", "mtext", "par", "plot", "plot.new")
  importFrom("utils", "data")
to your NAMESPACE file.
pass: no visible global function definition for 'predict'
plot.pass: no visible global function definition for 'par'
plot.pass: no visible global function definition for 'plot'
Undefined global functions or variables:
  par plot predict
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/pcadapt.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
cdfDist: no visible global function definition for 'tail'
cor2icc: no visible global function definition for 'cor'
plot.cdfDist: no visible global function definition for 'plot'
plot.cdfDist: no visible global function definition for 'lines'
plot.cdfDist: no visible global function definition for 'axis'
plot.cdfDist: no visible global function definition for 'mtext'
plot.cdfDist: no visible global function definition for 'legend'
Undefined global functions or variables:
  axis cor legend lines mtext plot tail
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "mtext", "plot")
  importFrom("stats", "cor")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'R.oo' 'limma' 'splines'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
fitBspline: no visible global function definition for 'median'
fitBspline: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'poisson'
fitGAPLM: no visible global function definition for 'quantile'
fitGAPLM: no visible global function definition for 'anova'
fitGAPLM: no visible global function definition for 'as.formula'
fitGAPLM: no visible global function definition for 'glm'
fitGAPLM: no visible global function definition for 'pf'
fitGAPLM: no visible global function definition for 'lm'
fitGAPLM: no visible global function definition for 'p.adjust'
head.DEresults: no visible global function definition for 'head'
head.plmDE: no visible global function definition for 'head'
hist.DEresults: no visible global function definition for 'hist'
hist.DEresults: no visible global function definition for 'colors'
hist.DEresults: no visible global function definition for 'box'
limmaPLM: no visible global function definition for 'quantile'
plot.DEresults: no visible global function definition for 'as.formula'
plot.DEresults: no visible global function definition for 'lm'
plot.DEresults: no visible global function definition for 'glm'
plot.DEresults: no visible global function definition for 'plot'
plot.DEresults: no visible global function definition for 'lines'
plot.DEresults: no visible global function definition for 'points'
plot.DEresults: no visible global function definition for 'predict'
Undefined global functions or variables:
  anova as.formula box colors glm head hist lines lm median p.adjust pf
  plot points poisson predict quantile
Consider adding
  importFrom("grDevices", "colors")
  importFrom("graphics", "box", "hist", "lines", "plot", "points")
  importFrom("stats", "anova", "as.formula", "glm", "lm", "median",
             "p.adjust", "pf", "poisson", "predict", "quantile")
  importFrom("utils", "head")
to your NAMESPACE file.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
Found the following significant warnings:
  congruRand.c:180:3: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:187:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:188:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
  congruRand.c:189:2: warning: ISO C does not support the 'I64' ms_scanf length modifier [-Wformat=]
See 'd:/Rcompile/CRANpkg/local/3.5/randtoolbox.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  Internal server error: java.lang.NullPointerException
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
    po    2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  > library('rdefra')
  > 
  > test_check('rdefra')
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 38 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 80.2Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.2Mb
    proj       5.0Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  libjson/Source/JSONGlobals.h:43:50: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONGlobals.h:44:49: warning: invoking macro json_global_decl argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  JSONValidator.cpp:394:105: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  JSONValidator.cpp:397:104: warning: invoking macro JSON_ASSERT_SAFE argument 3: empty macro arguments are undefined in ISO C90 and ISO C++98
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rpart/libs/i386/rpart.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rpart/libs/x64/rpart.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'test-all.R' [31s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  -- 1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  --------------
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  regTree.c:242:19: warning: suggest parentheses around comparison in operand of '&' [-Wparentheses]
See 'd:/Rcompile/CRANpkg/local/3.5/RRF.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSAP.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/RSEIS.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

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

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

Matrix products: default

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

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

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

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Running 'test-all.R' [33s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("rtext")
  Loading required package: rtext
  Loading required package: stringb
  -- 1. Error: rtext tokenize_data_words (@test_rtext.R#98)  ---------------------
  arguments must have same length
  1: expect_true({
         dings <- rtext$new("meine mudder schneidet speck - ho-narroh")
         dings$char_data_set("test", 1:5, 1)
         dings$char_data_set("toast", 1:dings$char_length(), "uggah")
         dings$char_data_get()
         length(dings$tokenize_data_words()$test) == 6
     }) at testthat/test_rtext.R:98
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: dings$tokenize_data_words() at testthat/test_rtext.R:103
  5: self$tokenize_data_regex(split = split, ignore.case = ignore.case, fixed = fixed, 
         perl = perl, useBytes = useBytes, non_token = non_token, join = join, aggregate_function = aggregate_function, 
         ...)
  6: self$tokenize_data_sequences(token = token, join = join, aggregate_function = aggregate_function, 
         ...)
  7: stats::aggregate(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  8: aggregate.data.frame(chardata[, -c(1:2)], by = list(token_i = token_i), FUN = "modus", 
         multimodal = NA, warn = FALSE)
  9: stop("arguments must have same length")
  
  == testthat results  ===========================================================
  OK: 281 SKIPPED: 0 FAILED: 1
  1. Error: rtext tokenize_data_words (@test_rtext.R#98) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
S3 methods shown with full name in documentation object 'cbind.rv':
  'cbind.rv' 'rbind.rv'

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  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/Ryacas.Rcheck/00install.out' for details.
plot.safidesign: no visible global function definition for 'par'
plot.safidesign: no visible global function definition for 'matplot'
plot.safidesign: no visible global function definition for 'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'colorRampPalette'
plot.safimodel : plot.coef: no visible global function definition for
  'barplot'
plot.safimodel : plot.coef: no visible global function definition for
  'axis'
plot.safimodel : plot.coef: no visible global function definition for
  'abline'
plot.safimodel : plot.coef: no visible global function definition for
  'box'
plot.safimodel: no visible global function definition for 'par'
safiModel: no visible global function definition for 'lm'
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Packages in Depends field not imported from:
  'datautils' 'irlba'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeKernel: no visible binding for global variable 'sd'
computeKernel: no visible global function definition for 'dist'
computeKernel: no visible global function definition for 'quantile'
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for 'irlba'
distortions: no visible binding for global variable 'sd'
distortions: no visible global function definition for 'dist'
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
plot.intersect: no visible global function definition for 'points'
plot.intersect: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'points'
plot.receiver: no visible global function definition for 'plot'
plot.receiver: no visible global function definition for 'segments'
plot.transmitter: no visible global function definition for 'points'
plot.transmitter: no visible global function definition for 'plot'
plot.transmitter: no visible global function definition for 'lines'
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
Running 'testthat.R' [45s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SimRVPedigree)
  > 
  > test_check("SimRVPedigree")
  -- 1. Failure: ascertained pedigrees meet number affected criteria (@test_ascert
  |... isn't true.
  
  == testthat results  ===========================================================
  OK: 74 SKIPPED: 2 FAILED: 1
  1. Failure: ascertained pedigrees meet number affected criteria (@test_ascertain_ped.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
plot.CorrAn : SAPplot: no visible global function definition for 'plot'
plot.CorrAn : SAPtitle: no visible global function definition for
  'title'
plot.CorrAn : SAPtitle: no visible global function definition for
  'mtext'
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  'points'
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  'text'
plot.CorrAn: no visible global function definition for 'dev.new'
plot.SimAn : SAPplot: no visible global function definition for 'plot'
plot.SimAn : SAPtitle: no visible global function definition for
  'title'
plot.SimAn : SAPtitle: no visible global function definition for
  'mtext'
plot.SimAn : SAPplotpuntos: no visible global function definition for
  'points'
plot.SimAn : SAPplotpuntos: no visible global function definition for
  'text'
plot.SimAn: no visible global function definition for 'dev.new'
plot.SimAn: no visible global function definition for 'points'
plot.SimAn: no visible global function definition for 'text'
plot.SimAn: no visible global function definition for 'par'
plot.SimAn: no visible global function definition for 'plot'
plot.SimAn: no visible global function definition for 'title'
plot.SimAn: no visible global function definition for 'axis'
plot.SimAn: no visible global function definition for 'arrows'
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
plot.sla: no visible global function definition for 'title'
plot.sla: no visible global function definition for 'abline'
print.sla: no visible global function definition for 'coef'
sla.default: no visible global function definition for 'lm'
sla.default: no visible global function definition for 'anova'
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
Packages in Depends field not imported from:
  'aqp' 'lattice' 'methods' 'munsell' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' call to 'rgdal' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'test-all.R' [207s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  -- 1. Failure: simList object initializes correctly (@test-simList.R#17)  --------------------------
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  == testthat results  ===========================================================
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/spatial/libs/i386/spatial.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/spatial/libs/x64/spatial.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.0Mb
    libs   1.2Mb
randomCorrelations: no visible global function definition for 'cor'
specGlm : <anonymous>: no visible global function definition for 'coef'
specLm : <anonymous>: no visible global function definition for 'coef'
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Package suggested but not available for checking: 'rcytoscapejs'
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    include   7.8Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'statnet'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'statnet'
See 'd:/Rcompile/CRANpkg/local/3.5/statnet.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.0/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.0/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Packages in Depends field not imported from:
  'cubature' 'deldir' 'splancs'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HRatio: no visible global function definition for 'qnorm'
icweib: no visible global function definition for 'model.frame'
icweib: no visible binding for global variable 'na.pass'
icweib: no visible global function definition for 'complete.cases'
icweib: no visible global function definition for 'model.matrix'
icweib: no visible global function definition for 'optim'
icweib: no visible global function definition for 'pchisq'
icweib: no visible global function definition for 'pnorm'
plot.icweib : getstat: no visible global function definition for
  'qnorm'
plot.icweib: no visible global function definition for 'plot'
plot.icweib: no visible global function definition for 'lines'
plot.icweib: no visible global function definition for 'legend'
print.icweib: no visible global function definition for 'pchisq'
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/stringi.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data    1.4Mb
    doc     2.6Mb
    tests   1.0Mb
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/survival/libs/i386/survival.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/survival/libs/x64/survival.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)

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.

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'tergm'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'tergm'
See 'd:/Rcompile/CRANpkg/local/3.5/tergm.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'grid' 'quadprog' 'maps' 'maptools' 'mapdata' 'dichromat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  'dichromat' 'grid' 'mapdata' 'maps' 'maptools' 'quadprog'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
plot.upclassfit: no visible global function definition for 'frame'
plot.upclassfit: no visible global function definition for 'par'
plot.upclassfit: no visible global function definition for 'axis'
plot.upclassfit: no visible global function definition for 'matplot'
plot.upclassfit: no visible global function definition for 'legend'
plot.upclassfit: no visible global function definition for 'title'
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
File 'webvis/R/zzz.R':
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

Package startup functions should use 'packageStartupMessage' to
  generate messages.
See section 'Good practice' in '?.onAttach'.

[1] "Welcome to the webvis pacakge."
render.webvis: no visible global function definition for 'browseURL'
unfold.webvis : <anonymous>: no visible global function definition for
  'runif'
Undefined global functions or variables:
  browseURL runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "browseURL")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.webvis':
  'plot.webvis'

S3 methods shown with full name in documentation object '"+.webvis"':
  '+.webvis'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    3.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ADM3.Rcheck/00install.out’ for details.
ADM3: no visible global function definition for ‘read.table’
ADM3: no visible global function definition for ‘write.table’
dLRs: no visible global function definition for ‘IQR’
dLRs: no visible global function definition for ‘na.omit’
dLRs: no visible global function definition for ‘qnorm’
plotADM3: no visible global function definition for ‘plot’
plotADM3: no visible global function definition for ‘abline’
plotADM3: no visible global function definition for ‘segments’
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AFM.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AIG.Rcheck/00install.out’ for details.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/amei.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/anapuce.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  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
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
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
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘apaStyle-Ex.R’ failed
The error most likely occurred in:

> ### Name: apa.descriptives
> ### Title: Generic method to generate an APA style table with descriptives
> ###   for MS Word.
> ### Aliases: apa.descriptives
> 
> ### ** Examples
> 
> 
> # Use apa.descriptives function
> apa.descriptives(
+   data = data.frame(
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1),
+     rnorm(100, mean = 0, sd = 1)
+   ),
+   variables = c("Column 1", "Column 2", "Column 3", "Column 4")
+ )
Error in .jnew(class.docx4r.document) : 
  java.lang.NoClassDefFoundError: javax/xml/bind/JAXBException
Calls: apa.descriptives ... apa.table.default -> apaStyleTable -> <Anonymous> -> .jnew
Execution halted
Package suggested but not available for checking: ‘testthat’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...

Returned 'NA'!


No TSN found for species 'Juniperus occidentalis'!


Retrieving data for taxon 'Pinus strobus'





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

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


Returned 'NA'!


No TSN found for species 'Pinus strobus'!


Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/aqr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TDA’
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Package unavailable to check Rd xrefs: ‘GLAD’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Arothron.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/audio.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
best: no visible global function definition for ‘optim’
randomboards: no visible global function definition for ‘runif’
randomprobs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

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

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/bamboo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANFF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANOVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   2.6Mb
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.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Execution halted
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Running ‘testthat.R’ [30s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: data.table
  > 
  > test_check("batchtools")
  ── 1. Failure: findConfFile (@test_findConfFile.R#7)  ──────────────────────────
  findConfFile() not equal to fs::path_abs(fn).
  1/1 mismatches
  x[1]: "/private/tmp/Rtmp2F3RCx/batchtools.conf.R"
  y[1]: "/tmp/Rtmp2F3RCx/batchtools.conf.R"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1453 SKIPPED: 7 FAILED: 1
  1. Failure: findConfFile (@test_findConfFile.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘mritc’

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/bayesCL.Rcheck/00install.out’ for details.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.0Mb
    libs   3.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    libs  60.5Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  15.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Depends: includes the non-default packages:
  ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

> ### Name: MLM.beadarray
> ### Title: Multi-level Mixed model
> ### Aliases: MLM.beadarray
> ### Keywords: differential expression
> 
> ### ** Examples
> 
> require(beadarrayExampleData)
Loading required package: beadarrayExampleData
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘beadarrayExampleData’
> data(exampleSummaryData)
Warning in data(exampleSummaryData) :
  data set ‘exampleSummaryData’ not found
> exampleSummaryDatalog2 <- channel(exampleSummaryData, "G")[1:40,]
Error in channel(exampleSummaryData, "G") : 
  object 'exampleSummaryData' not found
Execution halted
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
binommh.default : log_lik: no visible global function definition for
  ‘dbinom’
binommh.default: no visible global function definition for ‘dbinom’
binommh.default: no visible global function definition for ‘runif’
binommh.formula: no visible global function definition for
  ‘model.frame’
binommh.formula: no visible global function definition for
  ‘model.matrix’
binommh.formula: no visible global function definition for
  ‘model.response’
expmh.default : log_lik: no visible global function definition for
  ‘dexp’
expmh.default: no visible global function definition for ‘dexp’
expmh.default: no visible global function definition for ‘runif’
expmh.formula: no visible global function definition for ‘model.frame’
expmh.formula: no visible global function definition for ‘model.matrix’
expmh.formula: no visible global function definition for
  ‘model.response’
poissmh.default : log_lik: no visible global function definition for
  ‘dpois’
poissmh.default: no visible global function definition for ‘dpois’
poissmh.default: no visible global function definition for ‘runif’
poissmh.formula: no visible global function definition for
  ‘model.frame’
poissmh.formula: no visible global function definition for
  ‘model.matrix’
poissmh.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  141.0Mb
Running ‘testthat.R’ [1s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10006 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.6Mb
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
Package required but not available: ‘Rmpi’

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/BIGL.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot9164304db982.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot9164304db982.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
bigRR: no visible global function definition for ‘gaussian’
bigRR.default: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘as.formula’
bigRR.formula: no visible global function definition for ‘model.frame’
bigRR.formula: no visible global function definition for ‘model.matrix’
bigRR.formula: no visible global function definition for
  ‘model.response’
bigRR_update: no visible global function definition for ‘gaussian’
hugeRR: no visible global function definition for ‘gaussian’
hugeRR_update: no visible global function definition for ‘gaussian’
plot.bigRR: no visible global function definition for ‘par’
plot.bigRR: no visible global function definition for ‘plot’
plot.bigRR: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   7.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-44 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [7s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’ ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bioacoustics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Biocomb.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocStyle’
Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (IntroBiofiles.Rnw) 
Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Running ‘testthat.R’ [8s/29s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//README'
  Content type 'unknown' length 107 bytes
  ==================================================
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  Content type 'unknown' length 3574 bytes
  ==================================================
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 61 SKIPPED: 0 FAILED: 4
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: dependence (@test_install_uilts.R#88) 
  4. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

trying URL 'https://raw.githubusercontent.com/Miachol/ftp/master/files/GRCh37_MT_ensGene.txt'
Content type 'text/plain; charset=utf-8' length 3131 bytes
==================================================
downloaded 3131 bytes

Quitting from lines 102-109 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BioPhysConnectoR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for ‘na.omit’
extractPDB : read.pdb: no visible global function definition for
  ‘na.omit’
mat.read: no visible global function definition for ‘read.table’
mat.write: no visible global function definition for ‘write.table’
scpcp: no visible global function definition for ‘pgamma’
sim : sim.func: no visible global function definition for ‘write.table’
simc: no visible global function definition for ‘write.table’
simc : simc.func: no visible global function definition for
  ‘write.table’
sims: no visible global function definition for ‘write.table’
sims : sims.func: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 33.7Mb
  sub-directories of 1Mb or more:
    libs  33.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  conditional.least.squares.c:232:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:233:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
  conditional.least.squares.c:234:20: warning: absolute value function 'fabs' given an argument of type 'long double' but has parameter of type 'double' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bnlearn.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/boclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘sangerseqR’
installed size is 328.9Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      325.6Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bpca.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RGtk2’ ‘cairoDevice’
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    libs  31.3Mb
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2/3 mismatches
  x[2]: "c"
  y[2]: "b"
  
  x[3]: "b"
  y[3]: "c"
  
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 27 SKIPPED: 7 FAILED: 1
  1. Failure: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘pasilla’
Packages required but not available: ‘DiffBind’ ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  helpers.c:365:19: warning: absolute value function 'fabsf' given an argument of type 'double' but has parameter of type 'float' which may cause truncation of value [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BSquare.Rcheck/00install.out’ for details.
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  23.9Mb
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs  79.0Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb3c71d491160.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb3c71d491160.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cairoDevice.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.2-7 
Warning in engine$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 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.2Mb
Found the following significant warnings:
  slpcovis.cpp:381:12: 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/catlearn.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CCMnet.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Running examples in ‘census-Ex.R’ failed
The error most likely occurred in:

> ### Name: getCensus
> ### Title: Scrape US Census Data
> ### Aliases: getCensus
> 
> ### ** Examples
> 
> radius <- 5
> cities <- c("Boston", "Los Angeles")
> df <- getCensus(cities, radius)
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Boston&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Boston"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Los%20Angeles&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Los Angeles"
Error in `[.data.frame`(geo.reply, , c("locality", "lon", "lat")) : 
  undefined columns selected
Calls: getCensus -> [ -> [.data.frame
Execution halted
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/changepoint.np.Rcheck/00install.out’ for details.
Running ‘test_changepoints.R’ [1s/1s]
Running the tests in ‘tests/test_changepoints.R’ failed.
Last 13 lines of output:
  [1] 88 10
  [1] 12 10
  [1] 89 10
  [1] 11 10
  [1] 90 10
  [1] 10 10
  [1] 77 10
  [1] 23 10
  > stopifnot(changepoints_mod@changepoints == 77)
  > 
  > # test rank one
  > res_ro = rank_one(scp_data, init, update_w=0.1, regularizer=0.1)
  > stopifnot(res_ro$tau == 56)
  Error: res_ro$tau == 56 is not TRUE
  Execution halted
Package suggested but not available for checking: ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CHAT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in library.dynam(lib, package, package.lib):
 shared object 'plyr.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-44 (access_childes_db.Rmd) 
Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircE.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
CircE.Plot: no visible global function definition for ‘dev.new’
CircE.Plot: no visible global function definition for ‘par’
CircE.Plot: no visible global function definition for ‘plot’
CircE.Plot: no visible global function definition for ‘axis’
CircE.Plot: no visible global function definition for ‘title’
CircE.Plot: no visible global function definition for ‘text’
CircE.Plot: no visible global function definition for ‘points’
CircE.Plot: no visible global function definition for ‘abline’
CircE.Plot: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis dev.new par plot points segments text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "segments", "text", "title")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FRAPO’
Package unavailable to check Rd xrefs: ‘FRAPO’
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clpAPI.Rcheck/00install.out’ for details.
Packages required but not available: ‘rggobi’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Package unavailable to check Rd xrefs: ‘SingleCellExperiment’
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘SingleCellExperiment’
Error in .requirePackage(package) : 
  unable to find required package ‘SingleCellExperiment’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'SingleCellExperiment'
  Calls: <Anonymous> ... getClass -> getClassDef -> .classEnv -> .requirePackage
  Execution halted
Running ‘testthat.R’ [19s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning 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 143-147 (clustree.Rmd) 
Error: processing vignette 'clustree.Rmd' failed with diagnostics:
there is no package called 'SingleCellExperiment'
Execution halted
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/colourvision.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Combine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompetingRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: 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/CompRandFld.Rcheck/00install.out’ for details.
Found the following significant warnings:
  date.cpp:167:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ConvCalendar.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Package suggested but not available for checking: ‘ProData’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Error in re-building vignettes:
  ...

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

    legend

Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma


Attaching package: 'rmgarch'

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

    first, last

Quitting from lines 217-225 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
all(sapply(args, function(x) is.zoo(x) || !is.plain(x) || (is.plain(x) &&  .... is not TRUE
Execution halted
Running examples in ‘cowplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw_image
> ### Title: Draw an image
> ### Aliases: draw_image
> 
> ### ** Examples
> 
> # Use image as plot background
> p <- ggplot(iris, aes(x = Sepal.Length, fill = Species)) + geom_density(alpha = 0.7)
> ggdraw() +
+   draw_image("http://jeroen.github.io/images/tiger.svg") +
+   draw_plot(p + theme(legend.box.background = element_rect(color = "white")))
Error in magick_image_readpath(path, density, depth, strip) : 
  Magick: unable to open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmpephi1C/magick-79137e1BGimjmQbQJ': No such file or directory @ error/constitute.c/ReadImage/549
Calls: draw_image -> <Anonymous> -> magick_image_readpath
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: cowplot
Loading required package: ggplot2

Attaching package: 'cowplot'

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

    ggsave

Loading required package: grid
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: viridisLite
Quitting from lines 218-222 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
Magick: unable to open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpBHxdct/magick-80307qphDOiydIf8w': No such file or directory @ error/constitute.c/ReadImage/549
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cplexAPI.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error in re-building vignettes:
  ...
Warning in engine$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 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘clusterProfiler’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Rglpk’
Error in re-building vignettes:
  ...
  Used default patient IDs!
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Warning in Data(x = c(25, 50, 50, 75, 100, 100, 225, 300), y = c(0, 0, 0,  :
  Used default patient IDs!
Warning in Data(x = c(25, 50, 50, 75, 100, 100, 225, 300), y = c(0, 0, 0,  :
  Used best guess cohort indices!
Warning: Removed 658 rows containing non-finite values (stat_density).
Warning: Removed 828 rows containing non-finite values (stat_density).
Warning: Removed 1 rows containing missing values (geom_vline).
Warning: Removed 1 rows containing missing values (geom_text).

Timing stopped at: 149.6 1.468 254.9
Execution halted
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Running ‘spelling.R’ [8s/8s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [40s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      table
  
  
  [31m──[39m [31m1. Failure: checkInstalledPackages (@test-misc.R#208) [39m [31m──────────────────────[39m
  `checkInstalledPackages(c("not", "installed"))` threw an error with unexpected message.
  Expected match: "Missing required packages: \"not\" and \"installed\""
  Actual message: "Missing required packages: \"installed\""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2590 SKIPPED: 14 FAILED: 1
  1. Failure: checkInstalledPackages (@test-misc.R#208) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 76.0Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
    doc    4.1Mb
    libs  65.9Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cudaBayesreg.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cudiaDet: no visible global function definition for ‘model.frame’
cudiaDet: no visible global function definition for ‘model.response’
cudiaDet: no visible binding for global variable ‘sd’
cudiaDet: no visible global function definition for ‘rdirichlet’
cudiaDet: no visible global function definition for ‘rnorm’
cudiaDet: no visible global function definition for ‘lm.ridge’
plot.cudia: no visible global function definition for ‘par’
plot.cudia: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm.ridge model.frame model.response par plot rdirichlet rnorm sd
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "model.frame", "model.response", "rnorm", "sd")
to your NAMESPACE file.
Running examples in ‘curl-Ex.R’ failed
The error most likely occurred in:

> ### Name: curl_echo
> ### Title: Echo Service
> ### Aliases: curl_echo
> 
> ### ** Examples
> 
> h <- handle_setform(new_handle(), foo = "blabla", bar = charToRaw("test"),
+ myfile = form_file(system.file("DESCRIPTION"), "text/description"))
> formdata <- curl_echo(h)
Error in curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle) : 
  Callback aborted
Calls: curl_echo -> curl_fetch_memory
Execution halted
Running ‘spelling.R’ [1s/2s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [7s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("curl")
  This is libcurl version 7.43.0 with SecureTransport 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: echo large data (@test-echo.R#7)  ─────────────────────────────────
  Callback aborted
  1: curl::curl_echo(handle = handle) at testthat/test-echo.R:7
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 175 SKIPPED: 1 FAILED: 1
  1. Error: echo large data (@test-echo.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 19.5Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dartR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  iterator.cpp:138:17: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:12:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:30:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:48:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DatABEL.Rcheck/00install.out’ for details.
get_temporary_file_name: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages required but not available: ‘RGtk2’ ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot93c63522030b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot93c63522030b.png': No such file or directory
Quitting from lines 61-72 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 55.7Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  53.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning 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]="./webshotf8e743deb17f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf8e743deb17f.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10002 milliseconds
Calls: duke_deploy ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/debug.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

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

    cutree

Warning 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.

Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

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 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  DEploid/updateHap.cpp:670:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:678:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:681:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
  DEploid/updateHap.cpp:682:18: warning: explicitly assigning value of variable of type 'size_t' (aka 'unsigned long') to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DEploid.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    help   1.4Mb
    libs   1.5Mb
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking:
  ‘gurobi’ ‘Rcplex’ ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Running ‘has-devel.R’ [1s/2s]
  Running ‘test-that.R’ [136s/203s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
      setup
  
  ── 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 393 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  48.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.6Mb
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/diffusionMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error in globalVariables(c("C", "R", "key.row", "key.col", "label.row",  : 
  could not find function "globalVariables"
kf: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom
Consider adding
  importFrom("stats", "dbinom")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following hidden files and directories:
  .directory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
distSegment: no visible global function definition for ‘dist’
distShape: no visible global function definition for ‘dist’
distTriangle: no visible global function definition for ‘dist’
exactHausdorff: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dist
Consider adding
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
'library' or 'require' calls in package code:
  ‘FKF’ ‘dlm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading dodgr
Quitting from lines 117-144 (benchmark.Rmd) 
Error: processing vignette 'benchmark.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
Found the following significant warnings:
  gibbsclustersamplealpha.cc:95:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  gibbsclustersamplealpha.cc:140:9: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dpmixsim.Rcheck/00install.out’ for details.
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: 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/DPWeibull.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/drugCombo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot100643a05274.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot100643a05274.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   4.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dvfBm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘wmtsa’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘wmtsa’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  15.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘sdcTable’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘EBS/libs/EBS.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ecospat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 56.3Mb
  sub-directories of 1Mb or more:
    libs  55.6Mb
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/emIRT.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘rgdal’ ‘rgeos’
  All declared Imports should be used.
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

> ### Name: CInp2TS
> ### Title: Function to convert Constant Input to Time Series
> ### Aliases: CInp2TS
> ### Keywords: CInp2TS
> 
> ### ** Examples
> 
> library(EmiStatR)
> library(xts)
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> cinp.daily.dir  <- system.file("shiny/EmiStatR_inputCSO/inputCSO", package = "EmiStatR")
> cinp.daily.file <- paste(cinp.daily.dir, "/qs_factor.csv", sep="")
> cinp.weekly     <- list(mon=1, tue=.83, wed=.83, thu=.83, fri=1, sat=1.25, sun=1.25)  
> # factors average to 1
> cinp.seasonal   <- list(jan=.79, feb=.79, mar=1.15, apr=1.15, may=1.15, jun=1.15,
+                         jul=1.15, aug=1.15, sep=1.15, oct=1.15, nov=.79, dec=.79) 
> # factors average to 1
> 
> ts1 <- CInp2TS(cinp, prec, cinp.daily.file, cinp.weekly, cinp.seasonal)
Error in `[.xts`(cinp.ts.deltap, 1:nrow(P1), ) : subscript out of bounds
Calls: CInp2TS -> [ -> [.xts
Execution halted
Running ‘testthat.R’ [82s/134s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  18: as(set_TextType(methods_file), "description")
  19: .class1(object)
  20: set_TextType(methods_file)
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 78 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.5Mb
Note: found 23639 marked Latin-1 strings
Packages required but not available: ‘xcms’ ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EnvStats.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  input2.c:767:10: 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/epanet2toolkit.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiWeek.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Equalden.HD.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> ### Name: LModularity
> ### Title: L Modularity
> ### Aliases: LModularity
> 
> ### ** Examples
> 
> # A modular matrix:
> modules = matrix(c(rep(c(1, 0, 0), each = 5),
+ rep(c(0, 1, 0), each = 5),
+ rep(c(0, 0, 1), each = 5)), 15)
> cor.hypot = CreateHypotMatrix(modules)[[4]]
> hypot.mask = matrix(as.logical(cor.hypot), 15, 15)
> mod.cor = matrix(NA, 15, 15)
> mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
> mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
> diag(mod.cor) = 1
> mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric
> 
> LModularity(mod.cor)
Error in method(g, ...) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Calls: LModularity -> method
Execution halted
Running ‘testthat.R’ [173s/275s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: plyr
  ── 1. Error: LModularity resturn resonable results (@test.LModularity.r#12)  ───
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: expect_equal(modules, LModularity(mod.cor)[[2]]) at testthat/test.LModularity.r:12
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: LModularity(mod.cor)
  5: method(g, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20953 SKIPPED: 1 FAILED: 1
  1. Error: LModularity resturn resonable results (@test.LModularity.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘exams-Ex.R’ failed
The error most likely occurred in:

> ### Name: exams2openolat
> ### Title: Generation of Exams for OpenOLAT
> ### Aliases: exams2openolat
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## define an exams (= list of exercises)
> myexam <- list(
+   "boxplots",
+   c("tstat", "ttest", "confint"),
+   c("regression", "anova"),
+   c("scatterplot", "boxhist"),
+   "relfreq"
+ )
> 
> ## output directory
> mydir <- tempdir()
> 
> ## generate .zip with OpenOLAT test in temporary directory
> exams2openolat(myexam, n = 3, dir = mydir)
Loading required namespace: rmarkdown
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
Running examples in ‘excerptr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_excerpts
> ### Title: Clone the Excerpts Code from <URL: github.com>
> ### Aliases: get_excerpts
> 
> ### ** Examples
> 
> path <- file.path(tempdir(), "excerpts")
> get_excerpts(directory = path, force = TRUE)
cloning into '/tmp/RtmpTxZvco/excerpts'...
Error in git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch,  : 
  Error in 'git2r_clone': SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: get_excerpts -> <Anonymous> -> <Anonymous>
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("excerptr")
  cloning into '/tmp/RtmptozHYR'...
  ── 1. Error: get (@test_basic.R#9)  ────────────────────────────────────────────
  SSL error: error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
  1: get_excerpts(directory = tempdir()) at testthat/test_basic.R:9
  2: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  3: git2r::clone(url = "https://github.com/fvafrCU/excerpts/", branch = branch, local_path = directory)
  
  3
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Error: get (@test_basic.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    exiftool  12.3Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FACTscorer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fArma.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.9Mb
Found the following significant warnings:
  Rconnection.cc:347:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  Rconnection.cc:356:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FastRWeb.Rcheck/00install.out’ for details.
Note: information on .o files is not available
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
Found the following significant warnings:
  fcnn/level2.cpp:82:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:119:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:165:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FCNN4R.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.5Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Running ‘test-as-dgCMatrix.R’ [3s/4s]
  Running ‘test-empty_array.R’ [3s/4s]
  Running ‘test-existence_collision.R’ [2s/4s]
  Running ‘test-hash.mapping.R’ [2s/4s]
  Running ‘test-hashing.R’ [3s/4s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fifer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FisherEM.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘MASS’ ‘elasticnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

Depends: includes the non-default packages:
  ‘gWidgets’ ‘tcltk’ ‘tkrplot’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Package suggested but not available for checking: ‘devEMF’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fpc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘Rglpk’

Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/frailtyHL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
installed size is 22.1Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
add.p.value.legend: no visible global function definition for ‘legend’
cat.freq.post: no visible global function definition for ‘quantile’
draw.signif.post.boxes: no visible global function definition for
  ‘polygon’
plot.freqMAP: no visible global function definition for ‘layout’
plot.freqMAP: no visible global function definition for ‘plot’
plot.freqMAP: no visible global function definition for ‘points’
plot.freqMAP: no visible global function definition for ‘lines’
plot.freqMAP: no visible global function definition for ‘abline’
plot.freqMAP: no visible global function definition for ‘axTicks’
posterior.comparison.freqMAP: no visible global function definition for
  ‘quantile’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  abline axTicks layout legend lines plot points polygon quantile
  rgamma
Consider adding
  importFrom("graphics", "abline", "axTicks", "layout", "legend",
             "lines", "plot", "points", "polygon")
  importFrom("stats", "quantile", "rgamma")
to your NAMESPACE file.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Running examples in ‘funcy-Ex.R’ failed
The error most likely occurred in:

> ### Name: funcyOutList-class
> ### Title: Class '"funcyOutList"'
> ### Aliases: funcyOutList-class funcyOutList
> ### Keywords: classes
> 
> ### ** Examples
> 
> set.seed(2808)
> ds <- sampleFuncy(obsNr=30, k=4, timeNr=7)
> data <- Data(ds)
> clusters <- Cluster(ds)
> 
> res <- funcit(data=data, clusters=clusters, seed=2808,
+               methods=1:5, k=4, parallel=TRUE)
Warning in funclustWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  It is not possible to set a seed for method funclust.
4 :Loading required namespace: funHDDC
 * *4 : * * *Warning in funHDDCWrapper(data = data, k = k, reg = reg, regTime = regTime,  :
  Clustering with 4 classes is not possible. 3 clusters are used!
 *Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 3 classes is not possible. 2 clusters are used!

Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 2 classes is not possible. 1 clusters are used!
Warning in Funclustering::funclust(fd = fd, K = k, thd = thd, increaseDimension = increaseDimension,  :
  Convergence of the algorithm to a solution with at least one empty cluster.
            Restart or a choose a smaller value for K = 4
Warning in funHDDCWrapper(data, k, reg, regTime, funcyCtrlMbc, model = "AkBkQkDk",  :
  Clustering with 1 classes is not possible. 0 clusters are used!

Error in funcit(data = data, clusters = clusters, seed = 2808, methods = 1:5,  : 
  Method funHDDC : Clustering for this data not possible.
Execution halted
Running ‘testMethods.R’ [52s/57s]
Running the tests in ‘tests/testMethods.R’ failed.
Last 13 lines of output:
  + }
  Loading required package: flexclust
  Loading required package: grid
  Loading required package: lattice
  Loading required package: modeltools
  Loading required package: stats4
  Loading required package: splines
  Loading required namespace: Funclustering
  Loading required namespace: funHDDC
  5 : * *5 : * * * *
  5 : * * *
  
  Error in funcit(methods = methods, data = ds@data, k = k, clusters = ds@clusters,  : 
    Method funHDDC : Clustering for this data not possible.
  Execution halted
Package in Depends field not imported from: ‘genlasso’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dualpathFusedX.mod: no visible global function definition for
  ‘graph.adjacency’
dualpathFusedX.mod: no visible global function definition for
  ‘clusters’
dualpathFusedX.mod: no visible global function definition for ‘ginv’
dualpathFusedX.mod: no visible global function definition for
  ‘subcomponent’
dualpathFusedX.mod: no visible global function definition for ‘rBind’
fpca.nonscore.cluster: no visible global function definition for
  ‘kmeans’
fpca.score.cluster: no visible global function definition for ‘kmeans’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  clusters ginv graph.adjacency kmeans rBind rbinom subcomponent
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘ROI.plugin.glpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘doMPI’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.4Mb
installed size is 66.3Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
installed size is 49.5Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     46.3Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gdmp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘VariABEL’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.7Mb
Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’

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.
'library' or 'require' calls in package code:
  ‘DatABEL’ ‘genetics’ ‘haplo.stats’ ‘hglm’ ‘qvalue’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘GenABEL.data’ ‘MASS’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following Makefile(s) without a final LF:
  inst/unitTests/Makefile
Some ‘make’ programs ignore lines not ending in LF.
Package required but not available: ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
'library' or 'require' call to ‘mmap’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'User_manual.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `USenglish'. Either you misspelled it
(babel)                or the language definition file USenglish.ldf was not fo
und.

See the babel package documentation for explanation.
! Package babel Error: You haven't specified a language option.

See the babel package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geo.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Unexported objects imported by ':::' calls:
  ‘maps:::makepoly’ ‘maps:::mapgetg’ ‘maps:::mapgetl’ ‘maps:::mapname’
  See the note in ?`:::` about the use of this operator.
Error in setClass("Extent", representation(xmin = "numeric", xmax = "numeric",  : 
  could not find function "setClass"
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gettingtothebottom.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
example.alpha: no visible global function definition for ‘rnorm’
example.quadratic.approx: no visible global function definition for
  ‘rnorm’
generate_nnm: no visible global function definition for ‘rnorm’
generate_nnm: no visible global function definition for ‘rgamma’
generate_nnm: no visible global function definition for ‘dnorm’
plot_nnm: no visible global function definition for ‘stack’
testmatrix: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  dnorm rgamma rnorm stack
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm")
  importFrom("utils", "stack")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RGtk2’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GFORCE.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Missing values detected: (3%)
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Switching to 'nipals' method.
  ── 1. Failure: rgl works (@test_gge.R#162)  ────────────────────────────────────
  `{ ... }` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: rgl works (@test_gge.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb92b226b1dfb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb92b226b1dfb.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...

Backtrace for this error:
#0  0x123629579
#1  0x123628945
#2  0x7fff93ac4529
sh: line 1: 96924 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/RtmpLCaVyQ/x1317a8c540f25fd/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1235f6579
#1  0x1235f5945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Running ‘test-all.R’ [1s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  8: git2r::fetch(gitrepo, name = "github", credentials = credentials)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 8
  1. Error: Install a single package (@test_install.R#8) 
  2. Error: Install a single package, removing old install (@test_install.R#14) 
  3. Error: Install a single package w/o vignettes (@test_install.R#19) 
  4. Error: Install from a branch (@test_install.R#25) 
  5. Error: Install from a commit ref (@test_install.R#36) 
  6. Error: Install from a tag (@test_install.R#42) 
  7. Error: Install from a pull request (@test_install.R#49) 
  8. Error: (unknown) (@test_internal.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Found the following significant warnings:
  openssl.c:420:31: warning: incompatible pointer types assigning to 'int (*)(EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, unsigned int)' (aka 'int (*)(struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned int)') from 'int (EVP_CIPHER_CTX *, unsigned char *, const unsigned char *, size_t)' (aka 'int (struct evp_cipher_ctx_st *, unsigned char *, const unsigned char *, unsigned long)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/git2r.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package required but not available: ‘rtracklayer’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 40.7Mb
  sub-directories of 1Mb or more:
    libs  40.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Errors in running code in vignettes:
when running code in ‘openbugs.Rnw’
  ...
+     kResult = try(R2OpenBUGS::bugs(forBugs$ragged, inits = int2, 
+         model.file = "bym.txt", n.chain = 2, n.iter = .... [TRUNCATED] 

> if (!is.null(kResult)) {
+     kParams = restoreParams(kResult, forBugs$ragged)
+ }

  When sourcing ‘openbugs.R’:
Error: $ operator is invalid for atomic vectors
Execution halted
Error in re-building vignettes:
  ...
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs

Attaching package: ‘R2jags’

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

    traceplot

module glm loaded
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 60.4Mb
  sub-directories of 1Mb or more:
    libs  59.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/glpkAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 'intro.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Errors in running code in vignettes:
when running code in ‘GPPFourier.Rnw’
  ...
+     pch = 19, type = "b", xlab = "time", ylab = "GPP", xlim = as.POSIXct(c("2010-01-01 ..." ... [TRUNCATED] 

> par(mfrow = c(2, 1), cex = 2)

> plot(Kruibeke, pch = 20, xlim = as.POSIXct(c("2010-01-01", 
+     "2010-12-31")))

  When sourcing ‘GPPFourier.R’:
Error: figure margins too large
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPseq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
calc_chisq_statistic: no visible global function definition for ‘dpois’
generalized_poisson_likelihood: no visible global function definition
  for ‘var’
perform_permutation_de: no visible binding for global variable ‘rbinom’
perform_permutation_de: no visible global function definition for ‘var’
perform_permutation_ds: no visible binding for global variable ‘rbinom’
perform_permutation_ds: no visible global function definition for ‘var’
Undefined global functions or variables:
  dpois rbinom var
Consider adding
  importFrom("stats", "dpois", "rbinom", "var")
to your NAMESPACE file.
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Packages required but not available:
  ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
  ‘EnsDb.Mmusculus.v79’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘GenomicFeatures’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Running examples in ‘gtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: unByteCode
> ### Title: Convert a Byte-Code Function to an Interpreted-Code Function
> ### Aliases: unByteCode unByteCodeAssign assignEdgewise
> ### Keywords: programming utilites
> 
> ### ** Examples
> 
> datURL <- "https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659"
> dat <- as.matrix(read.csv(file=datURL, row.names=1))
Warning in file(file, "rt") :
  cannot open URL 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659': HTTP status was '500 Internal Server Error'
Error in file(file, "rt") : 
  cannot open the connection to 'https://bugs.r-project.org/bugzilla/attachment.cgi?id=1659'
Calls: as.matrix -> read.csv -> read.table -> file
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 29372 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpjUDYzi/x13717e8f67458/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x121f26579
#1  0x121f25945
#2  0x7fff93ac4529
Quitting from lines 33-34 (gunsales.Rmd) 
Error: processing vignette 'gunsales.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Package which this enhances but not available for checking: ‘RGtk2Extras’

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/h5.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 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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  8.9Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.14.1

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [61s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(heatwaveR)
  Loading required package: data.table
  Loading required package: ggplot2
  > 
  > test_check("heatwaveR")
  ── 1. Failure: robust = TRUE switches to the slower function (@test-ts2clm.R#59)
  t_2[1] is not strictly less than t_1[1]. Difference: 0.175
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 115 SKIPPED: 0 FAILED: 1
  1. Failure: robust = TRUE switches to the slower function (@test-ts2clm.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘XMLRPC’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HierO.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Highcharts (www.highcharts.com) is a Highsoft software product which is
not free for commercial and Governmental use
Quitting from lines 45-46 (charting-data-frames.Rmd) 
Error: processing vignette 'charting-data-frames.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/HMMpa.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package required but not available: ‘Rsamtools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘MenuCollection’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RGtk2’ ‘cairoDevice’ ‘RGtk2Extras’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘HTSFilter’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'application/x-eprint-tar' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.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/hypervolume.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.6Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: 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/IBDsim.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    5.8Mb
    libs  11.5Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘mixAK’
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
Quitting from lines 72-73 (Package_Introduction.Rmd) 
Error: processing vignette 'Package_Introduction.Rmd' failed with diagnostics:
object 'all_resid' not found
Execution halted
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.1Mb
Package suggested but not available for checking: ‘PROcess’
Package unavailable to check Rd xrefs: ‘PROcess’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IDTurtle.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  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/IFSPlot.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  12.8Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     17.0Mb
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpXpzF0q/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                AminusB               CminusD AminusB.minus.CminusD 
             0.04765402           -0.04765402            0.09530804 
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.03198493            0.03198493            0.12793972 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#26) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘rsprng’ ‘Rmpi’
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 29920 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2> /dev/null
Warning in system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
  running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprnnChM/x136d8f148a3659/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x123592579
#1  0x123591945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/intpoint.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
interior_point2d: no visible global function definition for ‘points’
random_problem: no visible global function definition for ‘runif’
show2d: no visible global function definition for ‘plot’
show2d: no visible global function definition for ‘abline’
show2d: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmcudaR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LambertW.Rcheck/00install.out’ for details.
installed size is 79.5Mb
  sub-directories of 1Mb or more:
    libs  78.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs          12.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Running ‘MASSch04.R’ [1s/1s]
Running the tests in ‘tests/MASSch04.R’ failed.
Complete output:
  > #-*- R -*-
  > 
  > ## Script from Fourth Edition of `Modern Applied Statistics with S'
  > 
  > # Chapter 4   Graphical Output
  > 
  > library(MASS)
  Error: package or namespace load failed for 'MASS' in gzfile(file, "rb"):
   cannot open the connection
  In addition: Warning message:
  In gzfile(file, "rb") :
    cannot open compressed file '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/MASS/data/Rdata.rdx', probable reason 'No such file or directory'
  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 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rtracklayer’
Errors in running code in vignettes:
when running code in ‘addTracks.Rnw’
  ...
+     flip = TRUE)

> ll <- LDheatmap(GIMAP5.CEU$snp.data, GIMAP5.CEU$snp.support$Position, 
+     flip = TRUE)

> grid.newpage()

  When sourcing ‘addTracks.R’:
Error: could not find function "grid.newpage"
Execution halted
get.cp: no visible global function definition for ‘cov’
heatmap: no visible global function definition for ‘image’
heatmap: no visible global function definition for ‘grey’
heatmap: no visible global function definition for ‘abline’
heatmap: no visible global function definition for ‘axis’
heatmap: no visible global function definition for ‘box’
ld_lasso: no visible global function definition for ‘cor’
ld_lasso_method: no visible global function definition for ‘pchisq’
plot_beta: no visible global function definition for ‘plot’
plot_beta: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘par’
plot_ldlasso: no visible global function definition for ‘plot’
plot_ldlasso: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘points’
trace.plot: no visible global function definition for ‘plot’
trace.plot: no visible global function definition for ‘lines’
trace.plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis box cor cov grey image lines par pchisq plot points
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "plot", "points")
  importFrom("stats", "cor", "cov", "pchisq")
to your NAMESPACE file.
chisqfit: no visible global function definition for ‘hist’
drawsample: no visible global function definition for ‘runif’
fitdistribution: no visible global function definition for ‘optimize’
fitdistribution: no visible global function definition for ‘var’
fthetacum: no visible global function definition for ‘integrate’
fthetaf: no visible global function definition for ‘dbeta’
plot.angledist: no visible global function definition for ‘hist’
plot.angledist: no visible global function definition for ‘curve’
plot.angledist: no visible global function definition for ‘box’
plot.angledistlist: no visible global function definition for ‘pdf’
plot.angledistlist: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  box curve dbeta dev.off hist integrate optimize pdf runif var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "box", "curve", "hist")
  importFrom("stats", "dbeta", "integrate", "optimize", "runif", "var")
to your NAMESPACE file.
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/libstableR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [81s/38s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: raster::stack(save_in)
  5: raster::stack(save_in)
  6: .local(x, ...)
  7: .quickStackOneFile(x, bands = bands, native = native)
  8: brick(filename, native = native)
  9: brick(filename, native = native)
  10: .rasterObjectFromFile(x, objecttype = "RasterBrick", ...)
  11: stop("Cannot create a RasterLayer object from this file. (file does not exist)")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 248 SKIPPED: 0 FAILED: 1
  1. Error: grid_canopy returns a VRT (@test-grid_catalog.R#65) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error in re-building vignettes:
  ...
Warning 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 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
Found the following hidden files and directories:
  .DESCRIPTION.swo
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/liso.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘Iso’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'seq.log':
  ‘seq.log’

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 27.6Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.2Mb
    testdata   1.6Mb
mq.g.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Running examples in ‘lmem.gwaser-Ex.R’ failed
The error most likely occurred in:

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

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

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

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in plot.missing(crossobj) : could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LncPriCNet.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

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

> ### Name: confusion_stat
> ### Title: Display confusion or classification matrix following logistic
> ###   regression using glm with binomial family.
> ### Aliases: confusion_stat
> ### Keywords: models
> 
> ### ** Examples
> 
> library(MASS)
> library(LOGIT)
> data(R84)
> R84$cage <- R84$age - mean(R84$age)
> R84$cdoc <- R84$docvis - mean(R84$docvis)
> mylogit <- glm(outwork ~ cdoc + female + kids + cage + factor(edlevel),
+ family=binomial, data=R84)
> mu <- predict(mylogit, type="response")
> cutpoint<-ROCtest(mylogit, fold=10, type="Sensitivity")$cut
> mu[mu>=cutpoint]<-1
> mu[mu<cutpoint]<-0
> confusion_stat(mu, R84$outwork)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
Package suggested but not available for checking: ‘RDRToolbox’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  44.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.5Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MagneticMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1b95497e3633.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1b95497e3633.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd023306255d6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd023306255d6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘LPmerge’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.6Mb
plot.mathgraph: no visible global function definition for ‘plot’
plot.mathgraph: no visible global function definition for ‘box’
plot.mathgraph: no visible global function definition for ‘segments’
plot.mathgraph: no visible global function definition for ‘arrows’
plot.mathgraph: no visible global function definition for ‘text’
Undefined global functions or variables:
  arrows box plot segments text
Consider adding
  importFrom("graphics", "arrows", "box", "plot", "segments", "text")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ASGSCA’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Packages required but not available: ‘Rglpk’ ‘glpkAPI’

Package suggested but not available for checking: ‘cplexAPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.1Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

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

Execution halted

... incomplete output.  Crash?
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mdhglm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Loading required package: kinship2
Loading required package: quadprog
Loading required package: gdsfmt
Quitting from lines 694-696 (mega2rtutorial.Rmd) 
Error: processing vignette 'mega2rtutorial.Rmd' failed with diagnostics:
there is no package called 'TxDb.Hsapiens.UCSC.hg19.knownGene'
Execution halted
Packages required but not available: ‘RGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.6Mb
Packages suggested but not available for checking: ‘clpAPI’ ‘glpkAPI’ ‘ctc’
Running examples in ‘metaboGSE-Ex.R’ failed
The error most likely occurred in:

> ### Name: rescue
> ### Title: Rescue a model
> ### Aliases: rescue
> 
> ### ** Examples
> 
> data(Ec_core)
> rescue(Ec_core, target=0.1)
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: rescue ... optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Error in re-building vignettes:
  ...

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

    backsolve


groupGOTerms: 	GOBPTerm, GOMFTerm, GOCCTerm environments built.

Attaching package: 'topGO'

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

    members

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

    algorithm, algorithm<-, allGenes, genes

Loading required package: clpAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'clpAPI'
Quitting from lines 37-41 (metaboGSE.Rmd) 
Error: processing vignette 'metaboGSE.Rmd' failed with diagnostics:
package 'clpAPI' not found
Execution halted
Package required but not available: ‘rattle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘gWidgetsRGtk2’

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.
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Quitting from lines 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...
    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


> library(HTSFilter)

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

Attaching package: ‘DESeq’

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

    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 9 (label = DESeq1study) 
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
Execution halted
Found the following significant warnings:
  Warning: working directory was changed to ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MetaSubtract.Rcheck/MetaSubtract/extdata’, resetting
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: 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/mets.Rcheck/00install.out’ for details.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  13.9Mb
    misc   1.1Mb
Package suggested but not available for checking: ‘grasp2db’
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

> ### Name: assumptions.cmpoutput
> ### Title: Get assumptions for parametric tests performed on output
> ###   comparisons
> ### Aliases: assumptions.cmpoutput
> 
> ### ** Examples
> 
> 
> # Create a cmpoutput object from the provided datasets
> cmp <- cmpoutput("All", 0.9, pphpc_ok$data[["All"]], pphpc_ok$obs_lvls)
> 
> # Get the assumptions for the parametric tests performed in cmp
> acmp <- assumptions(cmp)
sROC 0.1-2 loaded
MANOVA assumptions require 'MVN' and 'biotools' packages.
Error in `*tmp*`[[i]] : subscript out of bounds
Calls: assumptions -> assumptions.cmpoutput
Execution halted
Running ‘testthat.R’ [19s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  subscript out of bounds
  1: assumptions(mic1a) at testthat/test_micomp.R:281
  2: assumptions.micomp(mic1a)
  3: lapply(obj, function(x) assumptions(x))
  4: FUN(X[[i]], ...)
  5: assumptions(x)
  6: assumptions.cmpoutput(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 363 SKIPPED: 0 FAILED: 2
  1. Error: assumptions.cmpoutput creates the correct object (@test_cmpoutput.R#214) 
  2. Error: micomp assumptions have the correct properties (@test_micomp.R#281) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
Execution halted
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Package suggested but not available for checking: ‘glpkAPI’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: lattice
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'glpkAPI'
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   5.3Mb
Packages suggested but not available for checking: ‘mixAK’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/missDeaths.Rcheck/00install.out’ for details.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Running examples in ‘mixKernel-Ex.R’ failed
The error most likely occurred in:

> ### Name: cim.kernel
> ### Title: Compute and display similarities between multiple kernels
> ### Aliases: cim.kernel
> 
> ### ** Examples
> 
> data(TARAoceans)
> 
> # compute one kernel per dataset
> phychem.kernel <- compute.kernel(TARAoceans$phychem, kernel.func = "linear")
> pro.phylo.kernel <- compute.kernel(TARAoceans$pro.phylo, kernel.func = "abundance")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: compute.kernel ... distance -> do.call -> do.call -> vegdist -> vegdist
Execution halted
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

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

        If installing GTK+ continues to be problematic, consider using the
        script version of MixSIAR. See manual for help and examples.
Execution halted
Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Failure: retune_abundance reproduces scaling model (@test-wrapper_function
  max(abs(initial_n - pr@initial_n)) is not strictly less than 2e-11. Difference: 1.09e-11
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 1 FAILED: 1
  1. Failure: retune_abundance reproduces scaling model (@test-wrapper_functions.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’
Package required but not available: ‘rsgcc’

Packages suggested but not available for checking:
  ‘GeneSelector’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘minfi’ ‘BiocStyle’
Error in re-building vignettes:
  ...
Warning 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 27-28 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Fbetaf.ct: no visible global function definition for ‘as’
Fbetaf.it: no visible global function definition for ‘as’
ci: no visible global function definition for ‘pnorm’
initial.values: no visible global function definition for ‘glm’
initial.values: no visible binding for global variable ‘binomial’
initial.values: no visible global function definition for ‘coef’
mseb: no visible global function definition for ‘rnorm’
mseb: no visible global function definition for ‘rmultinom’
msef.ct: no visible global function definition for ‘as’
msef.it: no visible global function definition for ‘as’
phi.direct: no visible global function definition for ‘as’
phi.direct.ct: no visible global function definition for ‘as’
phi.direct.it: no visible global function definition for ‘as’
Undefined global functions or variables:
  as binomial coef glm pnorm rmultinom rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "binomial", "coef", "glm", "pnorm", "rmultinom",
             "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MortHump.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
plot.Mposterior: no visible global function definition for ‘plot’
plot.Mposterior: no visible global function definition for ‘rainbow’
plot.Mposterior: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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
Packages required but not available: ‘mzR’ ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
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.
Package required but not available: ‘MSeasy’

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Running examples in ‘mssqlR-Ex.R’ failed
Errors in running code in vignettes:
when running code in ‘chfls1.Rnw’
  ...

> library("xtable")

> library("car")
Loading required package: carData

  When sourcing ‘chfls1.R’:
Error: package or namespace load failed for ‘car’ in library.dynam(lib, package, package.lib):
 shared object ‘readxl.so’ not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: carData

Error: processing vignette 'chfls1.Rnw' failed with diagnostics:
 chunk 1 (label = setup) 
Error : package or namespace load failed for ‘car’ in library.dynam(lib, package, package.lib):
 shared object ‘readxl.so’ not found
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 59.5Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MultiPhen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Undocumented S4 methods:
  generic '[<-' and siglist 'Multiplyr,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: length_of_stay
> ### Title: Estimates length of stay
> ### Aliases: length_of_stay
> 
> ### ** 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')
+ })
> 
> # New individual to estimate transition probabilities for
> newdata <- data.frame(age="20-40", dissub="AML")
> 
> # Estimate length of stay in each state after a year, given starting in state 1
> length_of_stay(models, 
+                newdata=newdata,
+                tmat, times=365.25,
+                start=1)

 *** caught illegal operation ***
address 0x10dab4b80, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, mat_exp, initial_times, start_states_long,     tcovs)
 2: individual_simulation(transitions, newdata_mat[i, ], trans_mat,     N, tcovs)
 3: FUN(X[[i]], ...)
 4: lapply(1:nrow(newdata_mat), function(i) {    individual_simulation(transitions, newdata_mat[i, ], trans_mat,         N, tcovs)})
 5: multiple_simulations(transition_list, trans_mat, attr_mat, N,     tcovs, label_df)
 6: state_occupancy(models, trans_mat, newdata, N, tcovs, ci, M)
 7: length_of_stay(models, newdata = newdata, tmat, times = 365.25,     start = 1)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Found the following significant warnings:
  ./index_heap.h:318:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/nabor.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
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 49-50 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
Unable to extract deviance function from model fit
Execution halted
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ncappc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/Sub-CommandLineArguments.Rmd’
   ‘vignettes/Sub-EstimatedNCAmetrics.Rmd’
   ‘vignettes/Sub-EstimationMethod.Rmd’
   ‘vignettes/Sub-Output.Rmd’
(Is a VignetteBuilder field missing?)
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.6Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  23: tryCatchList(expr, classes, parentenv, handlers)
  24: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  25: test_code(NULL, exprs, env)
  26: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  27: force(code)
  28: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  29: FUN(X[[i]], ...)
  30: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  31: force(code)
  32: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  33: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  34: 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)
  35: 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)
  36: test_check("NetworkInference")
  An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.5Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘dparser’ ‘inline’ ‘mvtnorm’ ‘vpc’
  All declared Imports should be used.
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.
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: model.frame(as.Formula(formula), as.data.frame(data), ..., rhs = rhs)
  11: model.frame.Formula(as.Formula(formula), as.data.frame(data), ..., rhs = rhs)
  12: model.frame(terms(formula, lhs = lhs, rhs = rhs, data = data, dot = dot), data = data, 
         ...)
  13: model.frame.default(terms(formula, lhs = lhs, rhs = rhs, data = data, dot = dot), 
         data = data, ...)
  14: eval(predvars, data, env)
  15: eval(predvars, data, env)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 55 SKIPPED: 0 FAILED: 1
  1. Error: mlogit object (@test_llcont.R#207) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/novelist.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
delta.star: no visible global function definition for ‘cov’
delta.star: no visible global function definition for ‘cov2cor’
hardt: no visible global function definition for ‘cov2cor’
novelist.assign: no visible global function definition for ‘cov2cor’
novelist.assign.inv: no visible global function definition for
  ‘cov2cor’
novelist.cov.cv: no visible global function definition for ‘cov’
novelist.cov.cv: no visible global function definition for ‘cor’
novelist.inv.cv: no visible global function definition for ‘cov’
novelist.inv.cv: no visible global function definition for ‘cor’
softt: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cor cov cov2cor
Consider adding
  importFrom("stats", "cor", "cov", "cov2cor")
to your NAMESPACE file.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/npcp.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘SweaveListingUtils’ ‘graphics’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
allsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for '<<-' assignment to ‘NAwarning’
cfuinterpolation: no visible binding for global variable
  ‘measured_values’
cfuinterpolation: no visible global function definition for ‘lm’
cfuinterpolation: no visible global function definition for ‘coef’
disconestep: no visible global function definition for ‘runif’
disconestep: no visible binding for global variable ‘measured_values’
disconestep: no visible binding for global variable ‘psteps’
makepdfoutput: no visible binding for '<<-' assignment to ‘textt’
makepdfoutput: no visible global function definition for ‘Sweave’
npmpm: no visible binding for '<<-' assignment to ‘inputsettings’
npmpm: no visible binding for global variable ‘psteps’
npmpm: no visible binding for '<<-' assignment to ‘cfu’
npmpm: no visible binding for '<<-' assignment to ‘countwarnings’
npmpm: no visible binding for global variable ‘cfu’
onestep: no visible binding for global variable ‘measured_values’
onestep: no visible global function definition for ‘var’
onestep: no visible binding for global variable ‘psteps’
onestep: no visible global function definition for ‘rnorm’
psteppar: no visible global function definition for ‘runif’
simpleinterpolation: no visible binding for global variable
  ‘measured_values’
Undefined global functions or variables:
  Sweave cfu coef lm measured_values psteps raw_data rnorm runif var
Consider adding
  importFrom("stats", "coef", "lm", "rnorm", "runif", "var")
  importFrom("utils", "Sweave")
to your NAMESPACE file.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   7.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
     
     taxi <- etl("nyctaxi", dir = "~/Desktop/nyctaxi/")
     taxi %>% 
        etl_extract(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_transform(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_load(years = 2016, months = 1:2, types = c("yellow","green")) 
     ## End(Not run)
     


Attaching package: 'lubridate'

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]="./webshot16f9f6d730a2b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16f9f6d730a2b.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    help   2.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  +   library(officer)
  +   library(magrittr)
  +   library(xml2)
  + })
  > 
  > test_check("officer")
  ── 1. Failure: test filename with accent (@test-zip.R#30)  ─────────────────────
  "filenameäüöß.pptx" %in% list.files(tempdir(), pattern = "^filename.*\\.pptx$") isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 457 SKIPPED: 1 FAILED: 1
  1. Failure: test filename with accent (@test-zip.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
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
Package suggested but not available for checking: ‘ROI.plugin.glpk’
Running examples in ‘ompr.roi-Ex.R’ failed
The error most likely occurred in:

> ### Name: with_ROI
> ### Title: Configures a solver based on 'ROI'
> ### Aliases: with_ROI
> 
> ### ** Examples
> 
> library(magrittr)
> library(ompr)
> library(ROI)
ROI.plugin.scs: R Optimization Infrastructure
Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, qpoases, quadprog, scs.
Default solver: auto.
> library(ROI.plugin.glpk)
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Running ‘testthat.R’ [13s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI.plugin.scs: R Optimization Infrastructure
  Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, qpoases, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
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 115.3Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    105.5Mb
    models    4.7Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: OpenMx
> ### Title: OpenMx: An package for Structural Equation Modeling and Matrix
> ###   Algebra Optimization
> ### Aliases: OpenMx OpenMx-package
> 
> ### ** Examples
> 
> library(OpenMx)
> data(demoOneFactor)
> # ===============================
> # = Make and run a 1-factor CFA =
> # ===============================
> 
> latents  = c("G") # the latent factor
> manifests = names(demoOneFactor) # manifest variables to be modeled
> # ====================
> # = Make the MxModel =
> # ====================
> m1 <- mxModel("One Factor", type = "RAM", 
+ 	manifestVars = manifests, latentVars = latents, 
+ 	mxPath(from = latents, to = manifests),
+ 	mxPath(from = manifests, arrows = 2),
+ 	mxPath(from = latents, arrows = 2, free = FALSE, values = 1.0),
+ 	mxData(cov(demoOneFactor), type = "cov", numObs = 500)
+ )
> 
> # ===============================
> # = mxRun it and get a summary! =
> # ===============================
> 
> m1 = mxRun(m1)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: mxRun -> runHelper
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘org.At.tair.db’
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
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘IsoGene’
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Found the following significant warnings:
  ccaRevolution.c:31:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:44:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:97:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:98:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:110:23: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ccaRevolution.c:111:27: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/osc.Rcheck/00install.out’ for details.
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10005 milliseconds
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rcplex’

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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PAactivPAL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘random_utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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 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
Warning: Column `party_id` joining character vector and factor, coercing into character vector
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]="./webshotc2552a92add0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2552a92add0.png': No such file or directory
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

Package suggested but not available for checking: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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 58-63 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
Operation was aborted by an application callback
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

Depends: includes the non-default packages:
  ‘svmpath’ ‘kernlab’ ‘affy’ ‘Biobase’ ‘ROCR’ ‘igraph’ ‘lpSolve’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Errors in running code in vignettes:
when running code in ‘pathClass.rnw’
  ...

    union

Loading required package: lpSolve

> library(golubEsets)

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

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, path, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Package required but not available: ‘pathview’

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.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdMPI.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
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 11.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.2Mb
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/PCRedux.Rcheck/00install.out’ for details.
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs    5.7Mb
    share  11.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pdolsms.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Peaks.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pendensity.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/penRvine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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.
dvol.mse.est: no visible global function definition for ‘optim’
ellipsoidSurface: no visible global function definition for ‘integrate’
latscale: no visible global function definition for ‘uniroot’
covariogram,Segment-function: no visible global function definition for
  ‘integrate’
plot,FigLat-missing: no visible global function definition for ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘lines’
plot,PointPattern-missing: no visible global function definition for
  ‘points’
plot,Quadrat-missing: no visible global function definition for ‘lines’
plot,Segment-matrix: no visible global function definition for ‘par’
plot,Segment-matrix: no visible global function definition for
  ‘polygon’
plot,Segment-missing: no visible global function definition for ‘lines’
Undefined global functions or variables:
  integrate lines optim par points polygon uniroot
Consider adding
  importFrom("graphics", "lines", "par", "points", "polygon")
  importFrom("stats", "integrate", "optim", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phalen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  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.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘run_tests.r’ [137s/253s]
Running the tests in ‘tests/run_tests.r’ failed.
Last 13 lines of output:
  Smoothing time series! 
  Merging Daymet Data! 
  Error : $ operator is invalid for atomic vectors
  Downloading: harvard_DB_0001_3day.csv
  Contracting Data! 
  Downloading: harvard_DB_0001_3day.csv
  ── 1. Failure: check download options (@test_download_function.r#64)  ──────────
  `check` isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 5 SKIPPED: 0 FAILED: 1
  1. Failure: check download options (@test_download_function.r#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘UsagePhenotypeSimulator.Rmd’, ‘UsagePhenotypeSimulator.html’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in 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
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Running examples in ‘phyloseqGraphTest-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph_perm_test
> ### Title: Performs graph-based permutation tests
> ### Aliases: graph_perm_test
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: graph_perm_test ... distance -> do.call -> do.call -> vegdist -> vegdist
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 128-134 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
"veg_distance" not available for .C() for package "vegan"
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhySortR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshota5993e30b266.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota5993e30b266.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
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 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.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

Package suggested but not available for checking: ‘latticist’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dyld: Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
  Reason: no suitable image found.  Did find:
	/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib: pread of first 4K failed: 0
	/Library/Frameworks/R.framework/Resources/lib/libgfortran.3.dylib: file too short
installed size is  8.5Mb
  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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pmlr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
pmlr: no visible global function definition for ‘model.response’
pmlr: no visible global function definition for ‘model.matrix’
pmlr: no visible global function definition for ‘model.weights’
pmlr: no visible global function definition for ‘pchisq’
pmlr: no visible global function definition for ‘qnorm’
profileCIs: no visible global function definition for ‘qchisq’
test.LR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  model.matrix model.response model.weights pchisq qchisq qnorm
Consider adding
  importFrom("stats", "model.matrix", "model.response", "model.weights",
             "pchisq", "qchisq", "qnorm")
to your NAMESPACE file.
Running examples in ‘PoloniexR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ReturnTradeHistory,PoloniexPublicAPI-method
> ### Title: Returns the past 200 trades for a given market, or up to 50,000
> ###   trades inside a specified input date range interval.
> ### Aliases: ReturnTradeHistory,PoloniexPublicAPI-method
> 
> ### ** Examples
> 
> Sys.setenv(tz = "UTC")
> poloniex.public <- PoloniexPublicAPI()
> pair   <- "BTC_NXT"
> from   <- as.POSIXct("2017-07-04 00:00:00 UTC")
> to     <- as.POSIXct("2017-07-05 00:00:00 UTC")
> 
> trades.data <- ReturnTradeHistory(theObject = poloniex.public,
+                                   pair      = pair,
+                                   from      = from,
+                                   to        = to)
Error in .ProcessRequest(request.str) : 
  Unable to connect to https://poloniex.com/public?command=returnTradeHistory&currencyPair=BTC_NXT&start=1499140800&end=1499227200 (404)
Calls: ReturnTradeHistory -> ReturnTradeHistory -> .ProcessRequest
Execution halted
Package suggested but not available for checking: ‘LPmerge’
Package unavailable to check Rd xrefs: ‘LPmerge’
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0      1.68      0.535           2 F    
 9            9         9    20      1      0.911    -0.555           2 F    
10           10        10    12      1      0.237     1.78            1 M    
# ... with more rows

> library(VariantAnnotation)

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

    select

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

    filter

Error in makeSchemaFromData(dna, "dna") : 
  ERROR: The names of the supplied data.frame need to be modified for the database see correct.df.names
Starting clinical
Starting samples
Starting dna
Warning: call dbDisconnect() when finished working with a connection
Error in filter_.Database(.data, .dots = compat_as_lazy_dots(...)) : 
  ERROR: Cannot uniquely map columns to table, try using: tableX.columnY
Starting gender
Starting clinical
Starting samples
Starting dna

Error: processing vignette 'poplite.Rnw' failed with diagnostics:
 chunk 15 
Error in library(VariantAnnotation) : 
  there is no package called ‘VariantAnnotation’
Execution halted
Packages suggested but not available for checking:
  ‘Rglpk’ ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’
Errors in running code in vignettes:
when running code in ‘ROI_vignette.Rnw’
  ...

> suppressMessages(library(ROI))

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

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

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

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

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

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

Error: processing vignette 'ROI_vignette.Rnw' failed with diagnostics:
 chunk 1 
Error in library(ROI.plugin.glpk) : 
  there is no package called ‘ROI.plugin.glpk’
Execution halted
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppcc.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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Ignoring unknown aesthetics: z
Warning: Ignoring unknown aesthetics: z
Warning in normalizePath(f2) :
  path[1]="./webshot1635920dad531.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1635920dad531.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/praznik.Rcheck/00install.out’ for details.
installed size is 14.0Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PROFANCY.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
getCandidates: no visible binding for global variable ‘envData’
getGraph: no visible binding for global variable ‘envData’
getProvidedDiseaseName: no visible binding for global variable
  ‘envData’
getSeed: no visible binding for global variable ‘envData’
getTopDiseaseMetabolites: no visible binding for global variable
  ‘envData’
Undefined global functions or variables:
  envData
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.2Mb
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Package suggested but not available for checking: ‘ALDEx2’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PsiHat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running ‘testthat.R’ [59s/59s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   Elapsed Time: 0.170667 seconds (Warm-up)
                 0.170965 seconds (Sampling)
                 0.341632 seconds (Total)
  
  .0%
  .33%
  .67%
  .100%
  1
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 136 SKIPPED: 0 FAILED: 1
  1. Failure: If it works. (@test-analyze.stanreg.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/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]="./webshot10c2a1b50db59.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10c2a1b50db59.png': No such file or directory
Quitting from lines 512-540 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Running ‘testthat.R’ [54s/84s]
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) : 91.9 | 91.6 | 4204302 (4204210)
  
  Duration: 1 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 252 SKIPPED: 0 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#39) 
  2. Failure: createReport (@test_computeQC.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Missing or unexported object: ‘batchtools::findConfFile’
Running examples in ‘pulsar-Ex.R’ failed
The error most likely occurred in:

> ### Name: findConfFile
> ### Title: find config file
> ### Aliases: findConfFile
> 
> ### ** Examples
> 
> ## Default config file provided by pulsar runs code in interactive mode
> ## This is for testing purposes and executes serially.
> findConfFile()
Error: 'findConfFile' is not an exported object from 'namespace:batchtools'
Execution halted
Running ‘testthat.R’ [31s/31s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  3: findConfFile(conffile)
  4: batchtools::findConfFile
  5: getExportedValue(pkg, name)
  6: stop(gettextf("'%s' is not an exported object from 'namespace:%s'", name, getNamespaceName(ns)), 
         call. = FALSE, domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 55 SKIPPED: 0 FAILED: 4
  1. Error: findConfFile (@test_batchtools.R#16) 
  2. Error: batch.pulsar options (@test_batchtools.R#50) 
  3. Error: weird lambda path results in correct error or warning 
  4. Error: (unknown) (@test_pulsar.R#31) 
  
  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.
Quitting from lines 173-174 (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pulsar.Rcheck/pulsar/CONTENT.Rmd) 
Quitting from lines 44-49 (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pulsar.Rcheck/pulsar/CONTENT.Rmd) 
Error: processing vignette 'pulsar.Rmd' failed with diagnostics:
'findConfFile' is not an exported object from 'namespace:batchtools'
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QoLR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  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.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QPot.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/qtbase.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  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 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.2Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
draw_legend: no visible global function definition for ‘legend’
draw_legend: no visible global function definition for ‘par’
draw_nodes: no visible global function definition for ‘lines’
draw_nodes: no visible global function definition for ‘points’
draw_nodes: no visible global function definition for ‘text’
draw_vertical_lines: no visible global function definition for ‘lines’
draw_vertical_lines: no visible global function definition for ‘abline’
layout_large_plot: no visible global function definition for ‘par’
layout_large_plot: no visible global function definition for ‘mtext’
layout_large_plot: no visible global function definition for ‘axis’
layout_large_plot: no visible global function definition for ‘lines’
layout_small_plot: no visible global function definition for ‘par’
rquipu: no visible global function definition for ‘colors’
rquipu: no visible global function definition for ‘jpeg’
rquipu: no visible global function definition for ‘png’
rquipu: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  abline axis colors dev.off jpeg legend lines mtext par png points
  text
Consider adding
  importFrom("grDevices", "colors", "dev.off", "jpeg", "png")
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "points", "text")
to your NAMESPACE file.
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ramidst.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   3.9Mb
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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RAppArmor.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Package suggested but not available for checking: ‘rpanel’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.7Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Package suggested but not available for checking: ‘rattle’
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘odfWeave’ ‘playwith’ ‘rggobi’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Errors in running code in vignettes:
when running code in ‘rbiouml.Rnw’
  ...
filterExpression Expression in JavaScript like 'ColumnName1 > 5 && ColumnName2 < 0'
filteringMode                                                  Which rows to select
outputPath                                               Path to the filtered table

> biouml.analysis("Filter table", list(inputPath = "data/Examples/Optimization/Data/Experiments/exp_data_1", 
+     filterExpression = "time < 40", ou .... [TRUNCATED] 

  When sourcing ‘rbiouml.R’:
Error: Internal server error: java.lang.NullPointerException
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calls with DUP:
   .Call("hclust_from_distance", data = as.double(x), size = as.integer(attributes(x)$Size), 
       link = as.integer(method), DUP = FALSE, NAOK = FALSE, PACKAGE = "Rclusterpp")
   .Call("hclust_from_data", data = x, link = as.integer(method), 
       dist = as.integer(distance), p = as.numeric(p), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "Rclusterpp")
DUP is no longer supported and will be ignored.
Rclusterpp.package.skeleton: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$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 62-65 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.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/Rcplex.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/RcppAPT.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
    libs      1.6Mb
Running ‘doRUnit.R’ [132s/133s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  test.as.dgr2dgc: (5 checks) ... OK (0.01 seconds)
  test.as.dgt2dgc: (18 checks) ... OK (0.09 seconds)
  test.as.dsc2dgc: (8 checks) ... OK (0.03 seconds)
  test.as.dsr2dgc: (4 checks) ... OK (0.03 seconds)
  test.as.dst2dgc: (2 checks) ... OK (0.01 seconds)
  test.as.dtc2dgc: (5 checks) ... OK (0.02 seconds)
  test.as.dtr2dgc: (4 checks) ... OK (0.02 seconds)
  test.as.dtt2dgc: (4 checks) ... OK (0.03 seconds)
  test.as.ind2dgc: (9 checks) ... OK (0.05 seconds)
  test.as.p2dgc: (5 checks) ... OK (0.02 seconds)
  test.as.stm2dgc: (1 checks) ... OK (0 seconds)
  test.as.stm2stm: (1 checks) ... OK (0 seconds)
  test.stop: (7 checks) ... OK (0.04 seconds)
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppArmadillo-unitTests.Rnw’
  ...

> if (err$nFail > 0) stop(sprintf("unit test problems: %d failures", 
+     err$nFail))

> if (err$nErr > 0) stop(sprintf("unit test problems: %d errors", 
+     err$nErr))

  When sourcing ‘RcppArmadillo-unitTests.R’:
Error: unit test problems: 1 errors
Execution halted
Error in re-building vignettes:
  ...
Error in rmultinom(n, size, prob) : NA in probability vector
Error in rmultinomC(n, size, prob) : c++ exception (unknown reason)
Error in rmultinom(n, size, prob) : no positive probabilities
Error in rmultinomC(n, size, prob) : c++ exception (unknown reason)
Timing stopped at: 0.009 0 0.009
Error : $ operator not defined for this S4 class
Error : Only CSC, COO and CSR matrices from SciPy are supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.

Error: processing vignette 'RcppArmadillo-unitTests.Rnw' failed with diagnostics:
 chunk 2 (label = unitTesting) 
Error in eval(expr, .GlobalEnv) : unit test problems: 1 errors
Execution halted
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppCWB.Rcheck/00install.out’ for details.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     23.0Mb
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      24.0Mb
    libs      8.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.5Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    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/RcppRedis.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/rcqp.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/rcrypt.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Error in re-building vignettes:
  ...
  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

Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

Attaching package: 'units'

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

    %*%

Quitting from lines 161-186 (vignette.Rmd) 
Error: processing vignette '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/rDEA.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 packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.0
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: 'jsonlite'

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

    flatten

Joining, by = "carrier"
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-40 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RDieHarder.Rcheck/00install.out’ for details.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rdist.Rcheck/00install.out’ for details.
checkForVServer: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$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]="./webshotd14efb7b68.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd14efb7b68.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.4Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  14.0Mb
HanoiTower: no visible global function definition for ‘object.size’
plot.HanoiTower: no visible global function definition for ‘plot’
plot.HanoiTower: no visible global function definition for ‘polygon’
plot.HanoiTower: no visible global function definition for ‘text’
Undefined global functions or variables:
  object.size plot polygon text
Consider adding
  importFrom("graphics", "plot", "polygon", "text")
  importFrom("utils", "object.size")
to your NAMESPACE file.
Package required but not available: ‘GenomeGraphs’

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

Package which this enhances but not available for checking: ‘Rcplex’
Running examples in ‘relations-Ex.R’ failed
The error most likely occurred in:

> ### Name: choice
> ### Title: Relation-Based Choices
> ### Aliases: relation_choice
> ### Keywords: math
> 
> ### ** Examples
> 
> data("SVM_Benchmarking_Classification")
> ## Determine the three best classification learners in the above sense.
> relation_choice(SVM_Benchmarking_Classification, k = 3)
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Calls: relation_choice ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Errors in running code in vignettes:
when running code in ‘relations.Rnw’
  ...

> data("Felines")

> relations <- as.relation_ensemble(Felines)

> E <- relation_consensus(relations, "symdiff/E")

  When sourcing ‘relations.R’:
Error: there is no package called ‘Rglpk’
Execution halted
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: grid

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/relax.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/repeated.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 7
  1. Error: (unknown) (@test-docx-bookmarks.R#4) 
  2. Error: (unknown) (@test-docx-img.R#8) 
  3. Error: (unknown) (@test-docx-plot.R#10) 
  4. Error: (unknown) (@test-file-extensions.R#3) 
  5. Error: (unknown) (@test-flextable.R#30) 
  6. Error: (unknown) (@test-pptx-img.R#9) 
  7. Error: (unknown) (@test-pptx-plot.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [20s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 26
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: expression input works (@test-input.R#17) 
  5. Error: reprex: character input works (@test-input.R#23) 
  6. Error: reprex: file input works (@test-input.R#31) 
  7. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  8. Error: Circular use is detected before render (@test-input.R#47) 
  9. Error: Leading prompts are removed (@test-input.R#55) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
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
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
'library' or 'require' call to ‘pso’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    libs  28.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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 80.1Mb
  sub-directories of 1Mb or more:
    libs      77.3Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rglpk.Rcheck/00install.out’ for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    3.7Mb
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.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGoogleAnalytics.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

> ### Name: grmod
> ### Title: Interface for _gretl_ estimation commands
> ### Aliases: grmod
> 
> ### ** Examples
> 
> set.seed(13)
> dfr = data.frame(y = rnorm(20), x = rnorm(20))
> grmod("ols y 0 x --simple-print",dfr)

No valid gretl executable: no output is produced
Error: '/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpNZE4NO/mbundle4ef27a0e3e9.xml' does not exist.
Execution halted
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘gWidgetsRGtk2’

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/RGtk2.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 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:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computePvals.c:488:10: 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/ridge.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘magrittr’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/00install.out’ for details.
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.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RJSONIO.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘golubEsets’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    rmd   6.8Mb
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.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.0Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
Execution halted
Running ‘RMongo-Ex.R’ [4s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmosek.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/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.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.399 - 0.418 == -0.0196
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     92.6Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Found the following significant warnings:
  ./hammock.h:369:15: 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/robfilter.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SSOAP’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in covMcd(.) : could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Package required but not available: ‘clpAPI’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘test_deoptim.R’ [20s/31s]
Running the tests in ‘tests/test_deoptim.R’ failed.
Last 13 lines of output:
  + 
  +     rt( test_nlp_01() )
  +     rt( test_nlp_02() )
  +     rt( test_nlp_03() )
  + 
  +     if ( ROI_TEST_ERRORS > 0 ) {
  +         stop("ROI_Test_Error ", ROI_TEST_ERRORS, " occurred during testing.")
  +     }
  + }
  Error in test_nlp_03() : equal(solution(nlp), c(20, 11, 15)) is not TRUE
  In addition: Warning message:
  In (function (lower, upper, fn, constr = NULL, meq = 0, eps = 1e-05,  :
    maximum number of iterations reached without convergence
  Error: ROI_Test_Error 1 occurred during testing.
  Execution halted
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘ROI.plugin.glpk’ ‘ROI.plugin.symphony’

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ROracle.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.5Mb
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/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  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  12.2Mb
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 17.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.1Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

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

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/RQuantLib.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSAP.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 307-310 (article.Rnw) 
Error: processing vignette 'article.Rnw' failed with diagnostics:
Please run "rscala::scalaInstall()" or install Scala manually.
Execution halted
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSEIS.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Namespaces in Imports field not imported from:
  ‘binman’ ‘httr’
  All declared Imports should be used.
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.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
filterSD: no visible binding for global variable ‘sd’
filterSD: no visible global function definition for ‘quantile’
fit_lasso: no visible global function definition for ‘coef’
fit_prlasso: no visible global function definition for ‘coef’
rsig: no visible binding for global variable ‘mclapply’
rsig.all: no visible binding for global variable ‘mclapply’
rsig.all : <anonymous>: no visible global function definition for
  ‘flush.console’
rsig.all : <anonymous>: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Running examples in ‘rsolr-Ex.R’ failed
The error most likely occurred in:

> ### Name: SolrCore-class
> ### Title: SolrCore
> ### Aliases: class:SolrCore SolrCore-class name,SolrCore-method
> ###   ndoc,SolrCore-method schema schema,SolrCore-method
> ###   fieldNames,SolrCore-method version version,SolrCore-method SolrCore
> ###   docs docs,SolrCore-method read,SolrCore-method
> ###   eval,SolrQuery,SolrCore-method
> ###   eval,TranslationRequest,SolrCore-method facets facets,SolrCore-method
> ###   groupings groupings,SolrCore-method ngroup,SolrCore-method
> ###   update,SolrCore-method delete,SolrCore-method commit
> ###   commit,SolrCore-method purgeCache,SolrCore-method
> ###   show,SolrCore-method
> ### Keywords: methods classes
> 
> ### ** Examples
> 
>      solr <- TestSolr()
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
Error: failed to load sRGB colorspace file
Fatal error: error during cleanup

rm: /tmp/Rtmpffhvo1: Too many open files
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Found the following significant warnings:
  ssl.cpp:110:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:113:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:139:7: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:165:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:169:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:280:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:284:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:805:11: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ssl.cpp:809:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSSL.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/rstanarm.Rcheck/00install.out’ for details.
installed size is 205.1Mb
  sub-directories of 1Mb or more:
    libs  202.5Mb
Running ‘testthat.R’ [252s/415s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rstansim)
  Loading required package: Rcpp
  > 
  > test_check("rstansim")
  
   *** caught segfault ***
  address 0x107f89aa0, cause 'memory not mapped'
  
  Traceback:
   1: .Call(list(name = "CppObject__finalize", address = <pointer: 0x7fcf56212660>,     dll = list(name = "Rcpp", path = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x7fcf5620b0f0>,         info = <pointer: 0x7fcf5385df00>), numParameters = 2L),     <pointer: 0x7fcf53470440>, .pointer)
   2: x$.self$finalize()
   3: (function (x) x$.self$finalize())(<environment>)
  An irrecoverable exception occurred. R is aborting now ...
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
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.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
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.
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]="./webshot14ab5585194ff.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot14ab5585194ff.png': No such file or directory
Quitting from lines 84-89 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
installed size is 46.8Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
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.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxCEcolInf.Rcheck/00install.out’ for details.
Found the following significant warnings:
  yacas/src/obmalloc.cpp:584:23: warning: result of comparison of constant 384307168202282325 with expression of type 'unsigned int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Ryacas.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs    5.2Mb
    yacas   1.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SAENET.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
SAENET.nnet: no visible global function definition for ‘as.formula’
SAENET.nnet: no visible global function definition for ‘rnorm’
SAENET.train: no visible global function definition for ‘predict’
Undefined global functions or variables:
  as.formula predict rnorm
Consider adding
  importFrom("stats", "as.formula", "predict", "rnorm")
to your NAMESPACE file.
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 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
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 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 1 - 0 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SDMTools.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sdols.Rcheck/00install.out’ for details.
Running ‘cran-tests.R’ [2s/2s]
Running the tests in ‘tests/cran-tests.R’ failed.
Last 13 lines of output:
  
  
  Program received signal SIGTRAP: Trace/breakpoint trap.
  
  Backtrace for this error:
  #0  0x1230e5579
  #1  0x1230e4945
  #2  0x7fff93ac4529
  Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
  In addition: Warning messages:
  1: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4961ccbe9a/iofile -n -s 2>/dev/null' had status 133
  2: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4948f5a29f/iofile -n -s 2>/dev/null' had status 133
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.1Mb
    doc    1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
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.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

> ### Name: lastCached
> ### Title: Function to get the last Google Cache Date for a URL
> ### Aliases: lastCached
> 
> ### ** Examples
> 
> lastCached("https://www.r-project.org/")
Error in if (is.na(res)) { : argument is of length zero
Calls: lastCached
Execution halted
Packages required but not available: ‘rggobi’ ‘gWidgetsRGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   6.9Mb
Found the following significant warnings:
  vcf.c:253:15: 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/seqminer.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File ‘sequoia/libs/sequoia.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘sequoia.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘SingleCellExperiment’ ‘MAST’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 111.6Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs    96.7Mb
    sqlite   1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shallot.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    www   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 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   9.9Mb
Package required but not available: ‘BSgenome’

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.3Mb
Error in re-building vignettes:
  ...
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Shutting down cluster.
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Warning: Ignoring unknown aesthetics: position
Shutting down cluster.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 28.5Mb
  sub-directories of 1Mb or more:
    libs  27.2Mb
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SMCP.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.8Mb
Found the following significant warnings:
  ./Scythe_IDE.cpp:70:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:107:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:147:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:148:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:149:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:189:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:211:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:212:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:262:3: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:265:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./Scythe_IDE.cpp:266:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/smoothSurv.Rcheck/00install.out’ for details.
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Found the following significant warnings:
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:534:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:553:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:575:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/unicodeobject.h:593:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:173:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:174:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  /System/Library/Frameworks/Python.framework/Versions/2.7/include/python2.7/stringobject.h:175:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SnakeCharmR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SocialMediaLab.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, 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: 1.21 secs
Identifing all possible orderings..
Total run time: 0.86 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]="./webshotf9064431846f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf9064431846f.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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spaceExt.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Running ‘test-all.R’ [275s/483s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  ── 1. Error: 3 levels of parent and child modules load and show correctly (@test
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: moduleGraph(mySim, FALSE) at testthat/test-module-deps-methods.R:201
  2: moduleGraph(mySim, FALSE)
  3: cluster_optimal(grph)
  
    Using cached copy of burn event in fireSpread module
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 344 SKIPPED: 33 FAILED: 1
  1. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#201) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Loading required package: quickPlot
Loading required package: reproducible

Attaching package: 'reproducible'

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

    %>%

Loading required package: RColorBrewer
Loading required package: raster
Loading required package: sp
Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 357-361 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Namespaces in Imports field not imported from:
  ‘fastdigest’ ‘httr’
  All declared Imports should be used.
installed size is 32.9Mb
  sub-directories of 1Mb or more:
    libs  31.0Mb
package ‘Matrix’ exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘run-all.R’ [8s/35s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  4: callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper", "fit", formula, 
         data@sdf, tolower(family$family), family$link, tol, as.integer(maxIter), weightCol, 
         regParam, as.double(var.power), as.double(link.power), stringIndexerOrderType, 
         offsetCol)
  5: invokeJava(isStatic = TRUE, className, methodName, ...)
  6: handleErrors(returnStatus, conn)
  7: stop(readString(conn))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: create DataFrame from list or data.frame (@test_basic.R#26) 
  2. Error: spark.glm and predict (@test_basic.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
	at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3272)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3253)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
	at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3252)
	at org.apache.spark.sql.Dataset.collect(Dataset.scala:2722)
	at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:173)
	at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
	... 36 more
Quitting from lines 102-104 (sparkr-vignettes.Rmd) 
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
java.lang.IllegalArgumentException
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:449)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:432)
	at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230)
	at scala.collection.mutable.HashMap.foreachE
Execution halted
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Packages required but not available: ‘xcms’ ‘MAIT’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.5Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.4Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
Running examples in ‘stepwise-Ex.R’ failed
The error most likely occurred in:

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


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

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

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

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages required but not available: ‘Rglpk’ ‘MultAlloc’

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  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.4Mb
installed size is 33.1Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
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.
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
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
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.
Packages required but not available: ‘clipper’ ‘qpgraph’

Packages suggested but not available for checking:
  ‘graphite’ ‘curatedOvarianData’ ‘BiocStyle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 73.0Mb
  sub-directories of 1Mb or more:
    libs  72.1Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/svd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘svHttp’
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
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
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sybilEFBA.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking:
  ‘glpkAPI’ ‘cplexAPI’ ‘clpAPI’
Package unavailable to check Rd xrefs: ‘glpkAPI’
Running examples in ‘sybil-Ex.R’ failed
The error most likely occurred in:

> ### Name: SYBIL_SETTINGS
> ### Title: Set and Get sybil Parameters
> ### Aliases: SYBIL_SETTINGS SOLVER METHOD TOLERANCE MAXIMUM ALGORITHM
> ###   OPT_DIRECTION USE_NAMES PATH_TO_MODEL SOLVER_CTRL_PARM
> ### Keywords: optimize
> 
> ### ** Examples
> 
>   ## show all current parameters
>   SYBIL_SETTINGS()
$MODELORG_VERSION
[1] "2.0"

$SOLVER
[1] "glpkAPI"

$METHOD
[1] "simplex"

$TOLERANCE
[1] 1e-06

$MAXIMUM
[1] 1000

$ALGORITHM
[1] "fba"

$OPT_DIRECTION
[1] "max"

$USE_NAMES
[1] FALSE

$PATH_TO_MODEL
[1] "."

$SOLVER_CTRL_PARM
  NA
1 NA

>   
>   ## show current setting for "SOLVER"
>   SYBIL_SETTINGS("SOLVER")
[1] "glpkAPI"
> 
>   ## change current solver to glpkAPI
>   SYBIL_SETTINGS("SOLVER", "glpkAPI")
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 = value, method = "", probType = "",  : 
  package ‘glpkAPI’ not found
Calls: SYBIL_SETTINGS -> checkDefaultMethod
Execution halted
Errors in running code in vignettes:
when running code in ‘sybil.Rnw’
  ...
number of exchange reactions: 20

> optL <- optimizeProb(Ec_core, algorithm = "fba", retOptSol = FALSE)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’

  When sourcing ‘sybil.R’:
Error: package ‘glpkAPI’ not found
Execution halted
Error in re-building vignettes:
  ...
sybil::fluxVar          Flux Variability Analysis


Type '?PKG::FOO' to inspect entries 'PKG::FOO', or 'TYPE?PKG::FOO' for
entries like 'PKG::FOO-TYPE'.




reading model description, ... OK
reading metabolite list ... OK
parsing reaction list ... OK
GPR mapping ... OK
sub systems ... OK
prepare modelorg object ... OK
validating object ... OK
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: processing vignette 'sybil.Rnw' failed with diagnostics:
 chunk 13 
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SynergizeR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.3Mb
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component 11: Modes: character, numeric
  Component 11: Lengths: 1, 3
  Component 11: names for current but not for target
  Component 11: target is character, current is numeric
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 4
  1. Failure: COX (@test_COX.R#6) 
  2. Failure: HTC (@test_HTC.R#6) 
  3. Failure: ITC (@test_ITC.R#6) 
  4. Failure: PTC (@test_PTC.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.4Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tensorBF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is 39.3Mb
  sub-directories of 1Mb or more:
    libs       7.3Mb
    tessdata  31.0Mb
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.
OMP: Error #15: Initializing libomp.dylib, but found libomp.dylib already initialized.
OMP: Hint: This means that multiple copies of the OpenMP runtime have been linked into the program. That is dangerous, since it can degrade performance or cause incorrect results. The best thing to do is to ensure that only a single OpenMP runtime is linked into the process, e.g. by avoiding static linking of the OpenMP runtime in any library. As an unsafe, unsupported, undocumented workaround you can set the environment variable KMP_DUPLICATE_LIB_OK=TRUE to allow the program to continue to execute, but that may cause crashes or silently produce incorrect results. For more information, please see http://www.intel.com/software/products/support/.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
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
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  14: mutate_as_tbl(.data, !!!dot)
  15: mutate(d_tmp, ...)
  16: mutate.tbl_df(d_tmp, ...)
  17: mutate_impl(.data, dots)
  18: group_optimal()
  19: membership(cluster_optimal(graph = .G(), weights = weights))
  20: cluster_optimal(graph = .G(), weights = weights)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 268 SKIPPED: 0 FAILED: 2
  1. Error: grouping returns integer vector (@test-group.R#14) 
  2. Error: grouping returns integer of correct length (@test-group.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 685 SKIPPED: 0 FAILED: 3
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TimeMachine.Rcheck/00install.out’ for details.
.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  tmux not found
  1: stop("tmux not found") at testthat/test-server.R:3
  
  ── 3. Error: (unknown) (@test-session.R#3)  ────────────────────────────────────
  tmux not found
  1: stop("tmux not found") at testthat/test-session.R:3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-pipe.R#3) 
  2. Error: (unknown) (@test-server.R#3) 
  3. Error: (unknown) (@test-session.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package required but not available: ‘RGtk2’

Package suggested but not available for checking: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘tpr/libs/tpr.so’:
  Found ‘__ZNSt3__14cerrE’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 96-97 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
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 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 39.6Mb
  sub-directories of 1Mb or more:
    libs  39.2Mb
Running ‘testthat.R’ [47s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: date_time_to_tsp(wx[[1]])
  7: stop("time column needs to specified as the first date of the period", call. = FALSE)
  
  "blabla"
  ── 2. Failure: heuristic high frequency data works (@test_ts_high_freq.R#91)  ──
  `x` not equal to ts_df(ts_ts(x)).
  Component "time": Mean absolute difference: 86579
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 340 SKIPPED: 9 FAILED: 2
  1. Error: Latest tricky stuff works. (@test_tricky.R#9) 
  2. Failure: heuristic high frequency data works (@test_ts_high_freq.R#91) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘TSodbc’
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 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
Error in re-building vignettes:
  ...
Version 0.4-0 included new data defaults. See ?getSymbols.
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

This message is shown once per session and may be disabled by setting 
options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.


WARNING: There have been significant changes to Yahoo Finance data.
Please see the Warning section of '?getSymbols.yahoo' for details.

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot16c10df4f1d8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16c10df4f1d8.png': No such file or directory
Quitting from lines 37-64 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       22.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.2Mb
Found the following significant warnings:
  ursa.c:3252:37: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ursa.c:3252:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ursa.c:3252:75: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ursa.Rcheck/00install.out’ for details.
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning 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 92-93 (regress_intro.Rmd) 
Error: processing vignette 'regress_intro.Rmd' failed with diagnostics:
object 'ttodth' not found
Execution halted
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
Running ‘run.R’ [32s/49s]
Running the tests in ‘tests/run.R’ failed.
Last 13 lines of output:
  12/14 type.R: type_alike(sum, sd, vetr_settings(type.mode = 1))
                                                                                  
  12/14 type.R: type_alike(sum, c, vetr_settings(type.mode = 1))
                                                                                  
  12/14 type.R: type_alike(`&&`, `[`, vetr_settings(type.mode = 1))
                                                                                  
  Error: $ operator is invalid for atomic vectors
  In addition: Warning message:
  In FUN(X[[i]], ...) :
    DESCRIPTION file of package 'unitizer' is missing or broken
  | Unexpectedly exited before storing unitizer; if you were reviewing a unitizer 
  | changes to that unitizer were not saved.  Note that any unitizers you *
  | completed* review of should have been saved.
  
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    R      3.4Mb
    doc    1.2Mb
    help   2.7Mb
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
Error in re-building vignettes:
  ...
Warning 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 157-163 (using_visdat.Rmd) 
Error: processing vignette 'using_visdat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 54.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  52.3Mb
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 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wand.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/warbleR.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [28s/46s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: curl::curl_echo(h) at testthat/test-echo.R:14
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ── 2. Error: Echo a big file (@test-echo.R#51)  ────────────────────────────────
  Callback aborted
  1: curl::curl_echo(h) at testthat/test-echo.R:51
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Error: test echo from httpuv (@test-echo.R#14) 
  2. Error: Echo a big file (@test-echo.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘HotDeckImputation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Warning in initDict() :
  cannot find WordNet 'dict' directory: please set the environment variable WNHOME to its parent

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

Probably some imports need to be declared in the NAMESPACE file.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data  11.2Mb
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
Package required but not available: ‘rtracklayer’

Packages suggested but not available for checking: ‘GenomicScores’ ‘ggbio’

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: processing vignette 'modification.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Running ‘doRUnit.R’ [36s/56s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Mean relative difference: 8.173474e-05
  
  FAILURE in test.timeSeries_reclass: Error in checkIdentical(sample.timeSeries, reclass(try.xts(sample.timeSeries))) : 
    FALSE 
   
  FAILURE in test.timeSeries_reclass_subset_reclass_j1: Error in checkIdentical(sample.timeSeries[, 1], reclass(try.xts(sample.timeSeries))[,  : 
    FALSE 
   
  DEACTIVATED test.zoo_reclass: rownames are not kept yet in current xts-dev
  DEACTIVATED test.zoo_reclass_subset_reclass_j1: rownames are not kept yet in current xts-dev
  Error: 
  
  unit testing failed (#test failures: 17, #R errors: 0)
  
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/zstdr.Rcheck/00install.out’ for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/ads.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'cacheSweave:::metaChunkName' 'cacheSweave:::metaSetCreationTime'
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/audio.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   1.8Mb
Error in re-building vignettes:
  ...
Quitting from lines 33-35 (use-ballr.Rmd) 
Error: processing vignette 'use-ballr.Rmd' failed with diagnostics:
HTTP error 502.
Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   1.9Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 3 (http://www.fangraphs.com/guts.aspx?type=cn) 
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   3.6Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 143.8Mb
  sub-directories of 1Mb or more:
    include  142.9Mb
Running examples in 'BioInstaller-Ex.R' failed
The error most likely occurred in:

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-06-16 01:55:27] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'blkergm'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'blkergm'
See 'd:/Rcompile/CRANpkg/local/3.4/blkergm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BonEV.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     2.7Mb
    doc   2.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'btergm'
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'btergm'
See 'd:/Rcompile/CRANpkg/local/3.4/btergm.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Running examples in 'causalMGM-Ex.R' failed
The error most likely occurred in:

> ### Name: loadSampleData
> ### Title: Load Sample Dataset
> ### Aliases: loadSampleData
> 
> ### ** Examples
> 
> library(rJava)
> mgm_init()
[1] "Error: tetrad.jar not loaded"
> ds <- loadSampleData()
Error in .jfindClass(as.character(class)) : 
  java.lang.ClassNotFoundException
Calls: loadSampleData -> J -> jclassName -> .jfindClass -> .Call
Execution halted
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some 'make' programs ignore lines not ending in LF.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  'figure/glmnet-diagnostic.pdf', 'figure/roc-plot.pdf'
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Running examples in 'codebook-Ex.R' failed
The error most likely occurred in:

> ### Name: codebook_missingness
> ### Title: Codebook missingness
> ### Aliases: codebook_missingness
> 
> ### ** Examples
> 
> data("bfi")
> codebook_missingness(bfi)
Error in `rownames<-`(`*tmp*`, value = 28L) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: codebook_missingness -> md_pattern -> <Anonymous> -> rownames<-
Execution halted
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Missing or unexported object: 'utils::askYesNo'
Running 'spelling.R' [3s]
  Comparing 'spelling.Rout' to 'spelling.Rout.save' ... OK
  Running 'testthat.R' [47s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(curl)
  > 
  > test_check("curl")
  This is libcurl version 7.59.0 with OpenSSL/1.0.2n (WinSSL) 
  Using test server: http://hb.opencpu.org 
  -- 1. Failure: host_con works via and multi_fdset (@test-multi.R#165)  ---------
  multi_fdset(pool = pool)$reads has length 1, not length 2.
  
  -- 2. Failure: host_con works via and multi_fdset (@test-multi.R#165)  ---------
  multi_fdset(pool = pool)$reads has length 0, not length 1.
  
  == testthat results  ===========================================================
  OK: 174 SKIPPED: 1 FAILED: 2
  1. Failure: host_con works via and multi_fdset (@test-multi.R#165) 
  2. Failure: host_con works via and multi_fdset (@test-multi.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/dbmss.Rcheck/00install.out' for details.
Running 'test-all.R' [23s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("dcmr")
  Loading required package: dcmr
  -- 1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scor
  `rmse_class` is not strictly less than `tolerance`. Difference: 0.35
  
  == testthat results  ===========================================================
  OK: 119 SKIPPED: 0 FAILED: 1
  1. Failure: Test ScoreDCM outputs for Qmatrix with no interaction (@test_scoreDCM.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.4Mb
    libs   1.7Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'Rmosek'
Running 'has-devel.R' [2s]
  Running 'test-that.R' [81s]
Running the tests in 'tests/test-that.R' failed.
Complete output:
  > library(testthat)
  > test_check("devtools")
  Loading required package: devtools
  
  Attaching package: 'devtools'
  
  The following object is masked from 'package:testthat':
  
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 400 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: RSQLite
no column `person_id` provided, automatically generating unique person id's
pandoc.exe: Could not fetch img/main_bar.PNG
img/main_bar.PNG: openBinaryFile: does not exist (No such file or directory)
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS dextergui.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output dextergui.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 67
Error: processing vignette 'dextergui.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 33-35 (DIF_vignette.Rmd) 
Error: processing vignette 'DIF_vignette.Rmd' failed with diagnostics:
'rho' must be an environment not promise: detected in C-level eval
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs   3.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.count'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.count'
See 'd:/Rcompile/CRANpkg/local/3.4/ergm.count.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'ergm::colMeans.mcmc.list' by 'statnet.common::colMeans.mcmc.list' when loading 'ergm.ego'
  Warning: replacing previous import 'ergm::sweep.mcmc.list' by 'statnet.common::sweep.mcmc.list' when loading 'ergm.ego'
See 'd:/Rcompile/CRANpkg/local/3.4/ergm.ego.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.graphlets'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.graphlets'
See 'd:/Rcompile/CRANpkg/local/3.4/ergm.graphlets.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.rank'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.rank'
See 'd:/Rcompile/CRANpkg/local/3.4/ergm.rank.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'ergm.userterms'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'ergm.userterms'
See 'd:/Rcompile/CRANpkg/local/3.4/ergm.userterms.Rcheck/00install.out' for details.
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ess)
  > 
  > test_check("ess")
  -- 1. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Italy") not equal to c(1, 2, 6).
  Lengths differ: 4 is not 3
  
  -- 2. Failure: show_country_rounds returns correct rounds for countries (@test-s
  show_country_rounds("Spain") not equal to 1:7.
  Lengths differ: 8 is not 7
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 23 FAILED: 2
  1. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#100) 
  2. Failure: show_country_rounds returns correct rounds for countries (@test-show_.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LinkingTo' field is unused: package has no 'src' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'fivethirtyeight-Ex.R'
Running examples in 'forcats-Ex.R' failed
The error most likely occurred in:

> ### Name: fct_anon
> ### Title: Anonymise factor levels
> ### Aliases: fct_anon
> 
> ### ** Examples
> 
> gss_cat$relig %>% fct_count()
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
    libs   1.4Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  -- 1. Failure: Catch unit tests pass (@test-cpp.R#5)  --------------------------
  C++ unit tests:
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   is a Catch v1.9.6 host application.
  Run with -? for options
  
  -------------------------------------------------------------------------------
  Entropy tests | test-cpp.cpp
    Numeric entropy - comparsion with entropy package
  -------------------------------------------------------------------------------
  test-cpp.cpp:26
  ...............................................................................
  
  test-cpp.cpp:33: FAILED:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   2.7Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
Found the following significant warnings:
  Warning: S3 methods 'hist.glm.krige.bayes', 'image.glm.krige.bayes', 'persp.glm.krige.bayes', 'lines.covariomodel', 'plot.covariogram', 'summary.likGLSM', 'print.likGLSM', 'print.summary.likGLSM' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/glmmBUGS.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs

Attaching package: 'R2jags'

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

    traceplot

module glm loaded
To access larger datasets in this package, install the spDataLarge
package with: `install.packages('spDataLarge',
repos='https://nowosad.github.io/drat/', type='source'))`

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/GRCdata.Rcheck/00install.out' for details.
Packages required but not available:
  'EnsDb.Hsapiens.v86' 'EnsDb.Rnorvegicus.v79' 'EnsDb.Mmusculus.v79'
  'org.Rn.eg.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-34\unhbox\voidb@x \penalty \@M \ {}1.
4/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is 145.5Mb
  sub-directories of 1Mb or more:
    java  144.1Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(harvestr)
  > foreach::registerDoSEQ()
  > test_check("harvestr")
  -- 1. Failure: caching in reap with long sample (@test-caching.R#76)  ----------
  all(t2[1] <= t1[1]) isn't true.
  
  == testthat results  ===========================================================
  OK: 104 SKIPPED: 5 FAILED: 1
  1. Failure: caching in reap with long sample (@test-caching.R#76) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   5.4Mb
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  13.8Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     12.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpUVJPiH\ex_data943439732e0b.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpUVJPiH\ex_data943439732e0b.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
> # Basic usage with default arguments
> result = knockoff.filter(X, y, knockoffs=knockoffs,
+                            statistic=stat.stability_selection)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 89 99
> 
> # Advanced usage with custom arguments
> foo = stat.stability_selection
> k_stat = function(X, X_k, y) foo(X, X_k, y, fitfun=stabs::lars.lasso)
> result = knockoff.filter(X, y, knockoffs=knockoffs, statistic=k_stat)
> print(result$selected)
 [1] 15 22 27 28 29 31 34 45 59 61 65 89 99
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  65.59 1.76 67.4 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   2.2Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
Found the following significant warnings:
  Warning: replacing previous import 'ergm::colMeans.mcmc.list' by 'statnet.common::colMeans.mcmc.list' when loading 'latentnet'
  Warning: replacing previous import 'ergm::sweep.mcmc.list' by 'statnet.common::sweep.mcmc.list' when loading 'latentnet'
See 'd:/Rcompile/CRANpkg/local/3.4/latentnet.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(lucr)
  > 
  > test_check("lucr")
  -- 1. Failure: Simple amounts can be converted (@test_conversion.R#4)  ---------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12.00"
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
    libs      1.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MetaIntegrator.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running 'testthat.R' [23s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(MixSIAR)
  > 
  > test_check("MixSIAR")
  -- 1. Error: Killer whale ex works (@test_ex5_killerwhale.R#40)  ---------------
  Error in node X_iso[1,1:2]
  Invalid parent values
  
  1: capture.output(jags.inf <- run_model(run = run, mix, source, discr, model_filename, 
         alpha.prior = kw.alpha, resid_err, process_err)) at testthat/test_ex5_killerwhale.R:40
  2: evalVis(expr)
  3: withVisible(eval(expr, pf))
  4: eval(expr, pf)
  5: eval(expr, pf)
  6: run_model(run = run, mix, source, discr, model_filename, alpha.prior = kw.alpha, 
         resid_err, process_err)
  7: R2jags::jags(jags.data, inits = jags.inits, parameters.to.save = jags.params, model.file = model_filename, 
         n.chains = mcmc$chains, n.burnin = mcmc$burn, n.thin = mcmc$thin, n.iter = mcmc$chainLength, 
         DIC = mcmc$calcDIC)
  8: jags.model(model.file, data = data, inits = init.values, n.chains = n.chains, n.adapt = 0)
  
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 1
  1. Error: Killer whale ex works (@test_ex5_killerwhale.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.8Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Running 'testthat.R' [15s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
'library' or 'require' calls to packages already attached by Depends:
  'amap' 'clValid' 'cluster' 'fpc' 'xcms'
  Please remove these calls from your code.
'library' or 'require' call to 'tcltk' in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  'mzR' 'xcms'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
'library' or 'require' calls to packages already attached by Depends:
  'MSeasy' 'tcltk'
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  'grDevices' 'xcms'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.9Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.3Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc   8.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   2.4Mb
File 'obliclus/libs/i386/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'
File 'obliclus/libs/x64/obliclus.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'random_cluster_C.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'random_cluster_C.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
    libs   1.3Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(OECD)
  > 
  > test_check("OECD")
  <XMLInputError: XML content does not seem to be XML: ''>
  -- 1. Error: get_data_structure returns a list of data frame with positive lengt
  trying to get slot "concepts" from an object of a basic class ("NULL") with no slots
  1: get_data_structure(dataset) at testthat/tests.R:4
  2: data.frame(data_structure@concepts)
  
  <XMLInputError: XML content does not seem to be XML: ''>
  -- 2. Failure: get_dataset returns a data frame with positive length (@tests.R#1
  nrow(df) > 0 isn't true.
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: get_data_structure returns a list of data frame with positive length (@tests.R#4) 
  2. Failure: get_dataset returns a data frame with positive length (@tests.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 68-70 (oecd_vignette_main.Rmd) 
Error: processing vignette 'oecd_vignette_main.Rmd' failed with diagnostics:
trying to get slot "concepts" from an object of a basic class ("NULL") with no slots
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R        2.3Mb
    libs     5.9Mb
    models   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Running examples in 'osi-Ex.R' failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: certificate has expired
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(osrmr)
  > 
  > test_check("osrmr")
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  -- 1. Error: viaroute finds routes (@test-basic_functions.R#15)  ---------------
  $ operator is invalid for atomic vectors
  1: expect_equal(viaroute(lat1, lng1, lat2, lng2, F, api_version, localhost), 1560, tolerance = 300, 
         scale = 1) at testthat/test-basic_functions.R:15
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: viaroute(lat1, lng1, lat2, lng2, F, api_version, localhost)
  5: viaroute_api_v5(lat1, lng1, lat2, lng2, instructions, address)
  6: assertthat::assert_that(assertthat::is.number(res$routes[[1]]$duration))
  7: see_if(..., env = env, msg = msg)
  8: tryCatch({
         eval(assertion, env)
     }, assertError = function(e) {
         structure(FALSE, msg = e$message)
     })
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: doTryCatch(return(expr), name, parentenv, handler)
  12: eval(assertion, env)
  13: eval(assertion, env)
  14: assertthat::is.number(res$routes[[1]]$duration)
  
  == testthat results  ===========================================================
  OK: 11 SKIPPED: 1 FAILED: 1
  1. Error: viaroute finds routes (@test-basic_functions.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/palm.Rcheck/00install.out' for details.
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Running examples in 'phuse-Ex.R' failed
The error most likely occurred in:

> ### Name: cvt_list2df
> ### Title: Convert list to data frame
> ### Aliases: cvt_list2df
> 
> ### ** Examples
> 
>   a <- "https://github.com/phuse-org/phuse-scripts/raw/master"
>   b <- "development/R/scripts"
>   c <- "Draw_Dist2_R.yml"
>   f1 <- paste(a,b,c, sep = '/')
>   r1 <- read_yml(f1)
>   r2 <- cvt_list2df(r1)
Error in a[[k1]] : subscript out of bounds
Calls: cvt_list2df -> typeof
Execution halted
Found the following significant warnings:
  Warning: S3 method 'format.SQLiteConnection' was declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/pkgmaker.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.5Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'psycho-Ex.R'
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Error in re-building vignettes:
  ...
trying URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot open URL 'http://github.com/dobriban/pweight/raw/master/vignettes/iGWAS.cad.example.RData'
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rcom'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   2.3Mb
Running examples in 'raptr-Ex.R' failed
The error most likely occurred in:

> ### Name: make.DemandPoints
> ### Title: Generate demand points for RAP
> ### Aliases: make.DemandPoints
> 
> ### ** Examples
> 
> # load data
> data(cs_spp, cs_space)
> 
> # generate species points
> species.points <- randomPoints(cs_spp[[1]], n = 100, prob = TRUE)
> env.points <- raster::extract(cs_space, species.points)
> 
> # generate demand points for a 1d space using ks
> dps1 <- make.DemandPoints(points = env.points[,1], kernel.method = "ks")
> 
> # generate demand points for a 2d space using hypervolume
> dps2 <- make.DemandPoints(points = env.points,
+                           kernel.method = "hypervolume",
+                           samples.per.point = 10)

Building tree... 
done.
Ball query... 

done.
Error: !self$finished is not TRUE
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    libs   1.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Running examples in 'rcongresso-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch_despesas_deputado
> ### Title: Fetches expenditures from deputy
> ### Aliases: fetch_despesas_deputado
> 
> ### ** Examples
> 
> gastos_abel_mesquita <- fetch_despesas_deputado(id = 178957)
> gastos_abel_junho2017 <- fetch_despesas_deputado(id = 178957, ano = 2017, mes = 06, itens = -1)
Error in strsplit(., "/") : non-character argument
Calls: fetch_despesas_deputado ... eval -> _fseq -> freduce -> <Anonymous> -> strsplit
Execution halted
Running 'testthat.R' [144s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Not Empty (@test_deputados.R#44)  -------------------------------
  nrow(dep_gastos) != 0 isn't true.
  
  == testthat results  ===========================================================
  OK: 73 SKIPPED: 0 FAILED: 1
  1. Failure: Not Empty (@test_deputados.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs      1.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   6.4Mb
    libs      1.7Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  -- 1. Error: (unknown) (@test-1-data-structures.R#6)  --------------------------
  error reading from connection
  1: expect_that(is.data.frame(republika()), is_true()) at testthat/test-1-data-structures.R:6
  2: condition(object)
  3: expect_true(x)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: is.data.frame(republika())
  7: republika()
  8: readRDS(local_file)
  
  -- 2. Error: (unknown) (@test-2-code.R#6)  -------------------------------------
  error reading from connection
  1: obce_body() %>% filter(KOD_LAU1 == "CZ0100") at testthat/test-2-code.R:6
  2: eval(lhs, parent, parent)
  3: eval(lhs, parent, parent)
  4: obce_body()
  5: readRDS(local_file)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-1-data-structures.R#6) 
  2. Error: (unknown) (@test-2-code.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3
RCzechia: downloading remote dataset.
Quitting from lines 66-91 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
error reading from connection
Execution halted
Running 'testthat.R' [37s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library('testthat')
  > library('rdefra')
  > 
  > test_check('rdefra')
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 38 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'RedditExtractoR-Ex.R' failed
The error most likely occurred in:

> ### Name: user_network
> ### Title: User relationship network
> ### Aliases: user_network
> 
> ### ** Examples
> 
> # load libraries
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(RedditExtractoR)
> target_urls <- reddit_urls(search_terms="cats", subreddit="Art", cn_threshold=50)
> target_df <- target_urls %>% 
+ filter(num_comments==min(target_urls$num_comments)) %$% 
+ URL %>% reddit_content # get the contents of a small thread

  |                                                                            
  |                                                                      |   0%Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'

  |                                                                            
  |======================================================================| 100%
> network_list <- target_df %>% user_network(include_author=FALSE, agg=TRUE) # extract the network
Error in left_join_impl(x, y, by_x, by_y, aux_x, aux_y, na_matches) : 
  Can't join on 'response_to' x 'response_to' because of incompatible types (factor / logical)
Calls: %>% ... left_join -> left_join.tbl_df -> left_join_impl -> .Call
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.2Mb
    proj       5.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    rmd   6.7Mb
File 'RMC/libs/i386/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'
File 'RMC/libs/x64/RMC.dll':
  Found '_ZSt4cout', possibly from 'std::cout' (C++)
    Objects: 'RMC.o', 'predict.o'
  Found 'rand', possibly from 'rand' (C)
    Object: 'ap.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
Running 'test-all.R' [32s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > ###
  > library(testthat)
  > test_check('rphylotastic')
  Loading required package: rphylotastic
  -- 1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17)  --------------
  HTTP error 500.
  1: taxa_get_taxonomic_tree(taxa) at testthat/test_tree.R:17
  2: jsonlite::fromJSON(paste(get_base_url(), "gt/pt/get_tree?taxa=", taxa.string, sep = ""))
  3: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  4: parseJSON(txt, bigint_as_char)
  5: parse_con(txt, bigint_as_char)
  6: open(con, "rb")
  7: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Loading a tree from NCBI taxonomy (@test_tree.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.4/RQuantLib.Rcheck/00install.out' for details.
installed size is 23.2Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.4/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.4/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  17.3Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Ryacas.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/sclero.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
installed size is 93.4Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    gdal     3.9Mb
    libs    69.9Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    www   6.3Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Running 'test-all.R' [152s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'reproducible'
  
  The following object is masked from 'package:testthat':
  
      %>%
  
    Using cached copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module
  -- 1. Failure: simList object initializes correctly (@test-simList.R#17)  --------------------------
  length(out) not equal to 75.
  1/1 mismatches
  [1] 73 - 75 == -2
  
    Using cached copy of burn event in fireSpread module
  == testthat results  ===========================================================
  OK: 349 SKIPPED: 33 FAILED: 1
  1. Failure: simList object initializes correctly (@test-simList.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/sparr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/SpatialFloor.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.6Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'stability-Ex.R'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
Running examples in 'statnet.common-Ex.R' failed
The error most likely occurred in:

> ### Name: mcmc-utilities
> ### Title: Utility operations for 'mcmc.list' objects
> ### Aliases: mcmc-utilities colMeans.mcmc.list sweep.mcmc.list
> ###   lapply.mcmc.list
> 
> ### ** Examples
> 
> data(line, package="coda")
> summary(line) # coda

Iterations = 1:200
Thinning interval = 1 
Number of chains = 2 
Sample size per chain = 200 

1. Empirical mean and standard deviation for each variable,
   plus standard error of the mean:

        Mean     SD Naive SE Time-series SE
alpha 2.9876 0.4984  0.02492        0.02375
beta  0.7992 0.3367  0.01683        0.01597
sigma 0.9681 0.7413  0.03707        0.05653

2. Quantiles for each variable:

        2.5%    25%    50%    75% 97.5%
alpha 1.9650 2.7321 3.0188 3.2420 3.877
beta  0.1431 0.6039 0.7963 0.9925 1.470
sigma 0.4250 0.6158 0.7912 1.0752 2.560

> colMeans.mcmc.list(line) # "Method"
    alpha      beta     sigma 
2.9875644 0.7991864 0.9680519 
> ## Don't show: 
> stopifnot(isTRUE(all.equal(summary(line)$statistics[,"Mean"],colMeans.mcmc.list(line))))
> ## End(Don't show)
> data(line, package="coda")
> colMeans.mcmc.list(line)-1:3
    alpha      beta     sigma 
 1.987564 -1.200814 -2.031948 
> colMeans.mcmc.list(sweep.mcmc.list(line, 1:3))
    alpha      beta     sigma 
 1.987564 -1.200814 -2.031948 
> ## Don't show: 
> stopifnot(isTRUE(all.equal(colMeans.mcmc.list(sweep.mcmc.list(line, 1:3)), colMeans.mcmc.list(line)-1:3)))
> ## End(Don't show)
> data(line, package="coda")
> colMeans.mcmc.list(line)[c(2,3,1)]
     beta     sigma     alpha 
0.7991864 0.9680519 2.9875644 
> colMeans.mcmc.list(lapply.mcmc.list(line, `[`,,c(2,3,1)))
Error in NextMethod("[") : argument is missing, with no default
Calls: colMeans.mcmc.list ... as.mcmc.list -> lapply -> lapply -> FUN -> [.mcmc -> NextMethod
Execution halted
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'statnet'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'statnet'
See 'd:/Rcompile/CRANpkg/local/3.4/statnet.Rcheck/00install.out' for details.
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(stellaRbase)
  > 
  > options(scipen = 25)
  > 
  > test_check("stellaRbase")
  -- 1. Failure: Row counts are correct. (@test-getEffects_Account.R#33)  --------
  t2[["_embedded"]][["records"]] has length 3, not length 2.
  
  -- 2. Failure: Row counts are correct and consolidate between lists and data tab
  nrow(t8) not equal to 2.
  1/1 mismatches
  [1] 3 - 2 == 1
  
  -- 3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30)  ---
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  -- 4. Failure: Row counts consolidate between lists and data tables. (@test-getP
  nrow(t6) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  -- 5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  t2[["_embedded"]][["records"]] has length 2, not length 1.
  
  -- 6. Failure: Row counts consolidate between lists and data tables. (@test-getT
  nrow(t7) not equal to 1.
  1/1 mismatches
  [1] 2 - 1 == 1
  
  == testthat results  ===========================================================
  OK: 208 SKIPPED: 0 FAILED: 6
  1. Failure: Row counts are correct. (@test-getEffects_Account.R#33) 
  2. Failure: Row counts are correct and consolidate between lists and data tables. (@test-getEffects_Account.R#52) 
  3. Failure: Row counts are as expected. (@test-getPayments_Account.R#30) 
  4. Failure: Row counts consolidate between lists and data tables. (@test-getPayments_Account.R#39) 
  5. Failure: Row counts are as expected. (@test-getTransactions_Account.R#31) 
  6. Failure: Row counts consolidate between lists and data tables. (@test-getTransactions_Account.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/stringi.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'curatedOvarianData'
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    sql   8.6Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
    libs   1.5Mb
Found the following significant warnings:
  Warning: replacing previous import 'statnet.common::colMeans.mcmc.list' by 'ergm::colMeans.mcmc.list' when loading 'tergm'
  Warning: replacing previous import 'statnet.common::sweep.mcmc.list' by 'ergm::sweep.mcmc.list' when loading 'tergm'
See 'd:/Rcompile/CRANpkg/local/3.4/tergm.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.3Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    2.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs        4.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.7Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Running examples in 'WHO-Ex.R' failed
The error most likely occurred in:

> ### Name: get_data
> ### Title: Retrieve Data from the World Health Organization
> ### Aliases: get_data
> 
> ### ** Examples
> 
> df <- get_data("WHOSIS_000001")
Error in get_result(url) : Internal Server Error (HTTP 500).
Calls: get_data -> get_result -> <Anonymous>
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
Package suggested but not available for checking: ‘HH’
Packages suggested but not available for checking: ‘INLA’ ‘Rgraphviz’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    3.3Mb
Error in re-building vignettes:
  ...
Loading required package: Cairo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'abn_v1.0.2.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.33 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘aroma.affymetrix’ ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Packages in Depends field not imported from:
  ‘actuar’ ‘hypergeo’ ‘reliaR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘ActuDistns-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgumbeld
> ### Title: Gumbel pdf
> ### Aliases: dgumbeld
> ### Keywords: Gumbel distribution
> 
> ### ** Examples
> x=runif(10,min=0,max=1)
> y=dgumbeld(x)
Error in dgumbel(x, mu = mu, sigma = sigma) : 
  unused arguments (mu = mu, sigma = sigma)
Calls: dgumbeld -> ifelse
Execution halted
.amdai.initparam: no visible global function definition for ‘cov’
.amdat.initiparam: no visible global function definition for ‘cov’
amdai: no visible global function definition for ‘cov’
Undefined global functions or variables:
  cov
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data       2.8Mb
    pictures   2.1Mb
Packages suggested but not available for checking: ‘HiTC’ ‘snpStats’
Packages unavailable to check Rd xrefs: ‘HiTC’, ‘snpStats’
Missing or unexported object: ‘lmerTest::as_lmerModLmerTest’
Error in re-building vignettes:
  ...
Warning in adapt(pT = pT, iD = iD, SF = 1, phi = 0, cp = 0.9, theta = 4,  :
  Power may be lower than planned.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'algebraichaplo.tex' failed.
LaTeX errors:
! LaTeX Error: File `ngerman.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [square,comma, numbers,sort&compress]{natbib}   % numbers wor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'alleHap.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \setcounter
                {secnumdepth}{5}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/umsa.fd)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/natbib/natbib.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/psnfss/times.sty)

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

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.28 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on anchors.log.
make: *** [anchors.pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/anchors.Rcheck/vign_test/anchors") : 
  running 'make' failed
Execution halted
Package suggested but not available for checking: ‘org.Hs.eg.db’
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

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

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apsimr-basics.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: gWidgets
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'apt.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [pdftex]{graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=13: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=14: zs > maxKappa
Warning in method(..., k = k[i]) : k=15: zs > maxKappa
Warning in axis(1, at = a, ...) : "axes" is not a graphical parameter
Loading required package: grid
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'archetypes.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
Packages required but not available: ‘aroma.core’ ‘PSCBS’

Packages suggested but not available for checking: ‘aroma.light’ ‘GLAD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘Cairo’
Error in re-building vignettes:
  ...
  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: estimability
Loading required package: car

Attaching package: 'car'

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

    recode

Quitting from lines 95-107 (art-contrasts.Rmd) 
Error: processing vignette 'art-contrasts.Rmd' failed with diagnostics:
there is no package called 'Cairo'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.2Mb
Error in re-building vignettes:
  ...
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'asmapvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.34 \usepackage
                [titles]{tocloft}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ASPBay
Loading required package: hexbin
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ASPBay.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘devtools’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(devtools)
  Error in library(devtools) : there is no package called 'devtools'
  Execution halted
Package suggested but not available for checking: ‘rgdal’
Package suggested but not available for checking: ‘partitions’
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

Attaching package: ‘Brobdingnag’

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

    max, min, prod, range, sum

Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘partitions’
Warning in good(icons) :
  Good's method is for matrices with no NA entries.  Answer supplied is indicative only (but should provide an upper bound)
Error: processing vignette 'fishervig.Rnw' failed with diagnostics:
at fishervig.Rnw:753, could not find function "S"
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BACA.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: BACCO
Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Loading required package: approximator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'both_papers.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
Error in re-building vignettes:
  ...

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bamboo.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    2.3Mb
    libs   2.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.6Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr

Execution halted
Running ‘testthat.R’ [32s/49s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: data.table
  > 
  > test_check("batchtools")
  ── 1. Failure: findConfFile (@test_findConfFile.R#7)  ──────────────────────────
  findConfFile() not equal to fs::path_abs(fn).
  1/1 mismatches
  x[1]: "/private/tmp/Rtmp7kuZ9A/batchtools.conf.R"
  y[1]: "/tmp/Rtmp7kuZ9A/batchtools.conf.R"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1453 SKIPPED: 7 FAILED: 1
  1. Failure: findConfFile (@test_findConfFile.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
bridge.nmix.R: no visible global function definition for ‘rnorm’
draw.alpha: no visible global function definition for ‘runif’
draw.alpha: no visible global function definition for ‘dbeta’
draw.alpha.2: no visible global function definition for ‘runif’
draw.beta.2: no visible global function definition for ‘runif’
draw.sig2: no visible global function definition for ‘rgamma’
draw.tau: no visible global function definition for ‘rgamma’
draw.u: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘runif’
draw.w: no visible global function definition for ‘rgamma’
draw.w.marg: no visible global function definition for ‘runif’
draw.w.marg: no visible global function definition for ‘rgamma’
trace.beta: no visible global function definition for ‘plot’
trace.beta: no visible global function definition for ‘lines’
trace.beta: no visible global function definition for ‘legend’
trace.beta.mcmc: no visible global function definition for ‘sd’
trace.beta.mcmc: no visible binding for global variable ‘sd’
trace.beta.mcmc: no visible global function definition for ‘plot’
trace.beta.mcmc: no visible global function definition for ‘title’
trace.beta.mcmc: no visible global function definition for ‘hsv’
trace.beta.mcmc: no visible global function definition for ‘lines’
trace.beta.mcmc: no visible global function definition for ‘points’
Undefined global functions or variables:
  dbeta hsv legend lines plot points rgamma rnorm runif sd title
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "lines", "plot", "points", "title")
  importFrom("stats", "dbeta", "rgamma", "rnorm", "runif", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bayesCL.Rcheck/00install.out’ for details.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.4Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BayesianNetwork.Rcheck/00install.out’ for details.
installed size is 56.7Mb
  sub-directories of 1Mb or more:
    libs  55.9Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
 **********   MAMS Version 1.01********** 

Type MAMSNews() to see new features/changes/bug fixes.

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

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Depends: includes the non-default packages:
  ‘gplots’ ‘xtable’ ‘mnormt’ ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gtools’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘MASS’ ‘bayesm’ ‘boa’ ‘e1071’ ‘gplots’ ‘gtools’ ‘mnormt’ ‘xtable’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  13.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: splines
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbefkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bbemkr.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘R2jags’ ‘INLA’
Running examples in ‘BCEA-Ex.R’ failed
The error most likely occurred in:

> ### Name: evppi
> ### Title: Expected Value of Perfect Partial Information (EVPPI) for
> ###   selected parameters
> ### Aliases: evppi evppi.default
> ### Keywords: Health economic evaluation Expected value of partial
> ###   information
> 
> ### ** Examples
> 
> # See Baio G., Dawid A.P. (2011) for a detailed description of the 
> # Bayesian model and economic problem
> #
> # Load the processed results of the MCMC simulation model
> data(Vaccine)
Warning: namespace ‘rjags’ is not available and has been replaced
by .GlobalEnv when processing object ‘vaccine’
> # 
> # Runs the health economic evaluation using BCEA
> m <- bcea(e,c,ref=2,interventions=treats)
> #
> # Computes the EVPPI for a bunch of parameters
> inp <- CreateInputs(vaccine)
Error in CreateInputs(vaccine) : 
  You need to install the package 'R2jags'. Please run in your R terminal:
 install.packages('R2jags')
Execution halted
Package suggested but not available for checking: ‘R2jags’
Running examples in ‘BCEs0-Ex.R’ failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Error in re-building vignettes:
  ...
Loading required package: plyr
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Warning in replayPlot(x) :
  plot type 'black' will be truncated to first character
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bcpa.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘beadarrayExampleData’
plot.asr: no visible global function definition for ‘plot’
plot.casr: no visible global function definition for ‘plot’
plot.del: no visible global function definition for ‘plot’
plot.q: no visible global function definition for ‘plot’
plot.sr: no visible global function definition for ‘plot’
plot.trace1: no visible global function definition for ‘plot’
plot.trace2: no visible global function definition for ‘plot’
plot.trace3: no visible global function definition for ‘plot’
plot.trace4: no visible global function definition for ‘plot’
Undefined global functions or variables:
  plot
Consider adding
  importFrom("graphics", "plot")
to your NAMESPACE file.
installed size is 55.2Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
Namespace in Imports field not imported from: ‘jsonlite’
  All declared Imports should be used.
Package suggested but not available for checking: ‘Rgraphviz’
Package unavailable to check Rd xrefs: ‘graph’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bench.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
For more information on the usage of the BEQI2 tool, type: vignette("BEQI2")
Number of duplicated records: 1
These will be removed
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BEQI2.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.74 \allsectionsfont
                     {\sffamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    libs  25.0Mb
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: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BGLR-extdoc.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BHMSMAfMRIvignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {latexsym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [3s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10010 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to ‘mvtnorm’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘Rcpp’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘bifactorial/libs/bifactorial.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘misc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘krit.o’, ‘pv.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.5Mb
Packages in Depends field not imported from:
  ‘Matrix’ ‘glmnet’ ‘lattice’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
lasso.stars: no visible global function definition for ‘glmnet’
plot.stars: no visible global function definition for ‘par’
plot.stars: no visible global function definition for ‘plot’
plot.stars: no visible global function definition for ‘lines’
Undefined global functions or variables:
  glmnet lines par plot
Consider adding
  importFrom("graphics", "lines", "par", "plot")
to your NAMESPACE file.
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    libs  27.5Mb
Package suggested but not available for checking: ‘RODBC’
Error in re-building vignettes:
  ...
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in normalizePath(f2) :
  path[1]="./webshot15f511c4ec2b8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot15f511c4ec2b8.png': No such file or directory
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      5.1Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
Error in re-building vignettes:
  ...
Loading required package: diptest
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘Biocomb-Ex.R’ failed
The error most likely occurred in:

> ### Name: Calculate3D
> ### Title: Plot the 3D-ROC curve
> ### Aliases: Calculate3D
> ### Keywords: feature selection classification HUM values AUC values
> ###   missing values
> 
> ### ** Examples
> 
> data(leukemia72)
> # Basic example
> # class label must be factor
> leukemia72[,ncol(leukemia72)]<-as.factor(leukemia72[,ncol(leukemia72)])
> 
> xdata=leukemia72
> 
> indexF=names(xdata)[10]
> 
> indexClass=ncol(xdata)
> label=levels(xdata[,indexClass])
> indexLabel=label
> 
> out=CalculateHUM_seq(xdata,indexF,indexClass,indexLabel)
> HUM<-out$HUM
> seq<-out$seq
> out=CalculateHUM_ROC(xdata,indexF,indexClass,indexLabel,seq)
> Calculate3D(indexF,out$Sn,out$Sp,out$S3,out$optSn,out$optSp,out$optS3,
+ out$thresholds,HUM,indexLabel[seq])
Error in rgl.open(useNULL) : 
  Java called System.exit(130) requesting R to quit - trying to recover
Calls: Calculate3D -> clear3d -> .check3d -> open3d -> rgl.open -> .C
Execution halted
Running ‘test-all.R’ [7s/7s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [3s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: check_url_status(url)
  5: httr::GET(url) at /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/biolink.Rcheck/tests/testthat/helper-functions.r:4
  6: request_perform(req, hu$handle$handle)
  7: request_fetch(req$output, req$url, handle)
  8: request_fetch.write_memory(req$output, req$url, handle)
  9: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 103 SKIPPED: 7 FAILED: 1
  1. Error: Reference KEGG Pathway URL is valid (@test-links-kegg.r#7) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘GO.db’ ‘org.Hs.eg.db’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/BiSEp.Rcheck/00install.out’ for details.
Package required but not available: ‘copula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BMAmevt.tex' failed.
LaTeX errors:
! LaTeX Error: File `cases.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
GibbsIteration: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
File ‘BMN/libs/BMN.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘JunctionTree.o’, ‘pseudoLikelihood.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bms.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \setpapersize
                 {A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘graph’ ‘Rgraphviz’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bnstruct.tex' failed.
LaTeX errors:
! Package pdftex.def Error: File `child_crosses_1000-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `alarm_crosses_1000-eps-converted-to.pdf' not 
found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `hepar2_crosses_1000-eps-converted-to.pdf' not
 found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `andes_crosses-eps-converted-to.pdf' not found
.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/bomrang.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

    dexp, dgamma, dweibull, pexp, pgamma, pweibull, qexp, qgamma,
    qweibull, rexp, rgamma, rweibull

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

    precip

Loading required package: BoolNet
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BoolFilter.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Warning in structure(x$children, class = "XMLNodeList") :
  Calling 'structure(NULL, *)' is deprecated, as NULL cannot have attributes.
  Consider 'structure(list(), *)' instead.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BoolNet_package_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 322.8Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      319.5Mb
installed size is 68.2Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
boxplotdou.formula: no visible global function definition for
  ‘model.frame’
bxpdou: no visible global function definition for ‘rainbow’
bxpdou.abox: no visible global function definition for ‘rect’
bxpdou.abox: no visible global function definition for ‘segments’
bxpdou.abox: no visible global function definition for ‘points’
bxpdou.boxplot.stat: no visible global function definition for
  ‘boxplot’
bxpdou.sheer.color: no visible global function definition for
  ‘adjustcolor’
bxpdou.stats: no visible global function definition for ‘formula’
do.call.with.par: no visible global function definition for
  ‘modifyList’
only.graphic.pars: no visible global function definition for ‘par’
Undefined global functions or variables:
  adjustcolor boxplot formula model.frame modifyList par points rainbow
  rect segments
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "boxplot", "par", "points", "rect", "segments")
  importFrom("stats", "formula", "model.frame")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: scatterplot3d
Loading required package: rgl
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'latex_bpca.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {colortbl}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 30.0Mb
  sub-directories of 1Mb or more:
    libs  29.8Mb
Running ‘testthat.R’ [20s/20s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2/3 mismatches
  x[2]: "c"
  y[2]: "b"
  
  x[3]: "b"
  y[3]: "c"
  
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  [1] "liquid_normal" "solid_normal"  "solid_patient"
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 27 SKIPPED: 7 FAILED: 1
  1. Failure: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
combine_family_info: no visible binding for global variable ‘isFALSE’
no_sigma: no visible global function definition for ‘isFALSE’
resp_cens : prepare_cens: no visible global function definition for
  ‘isFALSE’
Undefined global functions or variables:
  isFALSE
Running ‘testthat.R’ [143s/143s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 995 SKIPPED: 1 FAILED: 19
  1. Failure: brm produces expected errors (@tests.brm.R#17) 
  2. Error: all S3 methods have reasonable ouputs (@tests.brmsfit-methods.R#235) 
  3. Error: self-defined functions appear in the Stan code (@tests.make_stancode.R#334) 
  4. Failure: invalid combinations of modeling options are detected (@tests.make_stancode.R#403) 
  5. Failure: invalid combinations of modeling options are detected (@tests.make_stancode.R#411) 
  6. Error: Stan code for multivariate models is correct (@tests.make_stancode.R#454) 
  7. Error: known standard errors appear in the Stan code (@tests.make_stancode.R#701) 
  8. Error: Stan code of response times models is correct (@tests.make_stancode.R#802) 
  9. Error: weighted, censored, and truncated likelihoods are correct (@tests.make_stancode.R#896) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Brundle.Rcheck/00install.out’ for details.
bs.design: no visible global function definition for ‘spline.des’
bshazard.default: no visible global function definition for
  ‘model.frame’
bshazard.default: no visible global function definition for
  ‘model.matrix’
bshazard.default: no visible global function definition for
  ‘model.response’
bshazard_fit: no visible global function definition for ‘aggregate’
bspois: no visible global function definition for ‘dpois’
bspois: no visible global function definition for ‘var’
bspois: no visible global function definition for ‘qnorm’
lines.bshazard: no visible global function definition for ‘lines’
plot.bshazard: no visible global function definition for ‘plot’
plot.bshazard: no visible global function definition for ‘lines’
print.bshazard: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dpois lines model.frame model.matrix model.response plot
  qnorm spline.des var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "aggregate", "dpois", "model.frame",
             "model.matrix", "model.response", "qnorm", "var")
to your NAMESPACE file.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is 77.2Mb
  sub-directories of 1Mb or more:
    libs  76.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Package suggested but not available for checking: ‘gsl’
installed size is 18.7Mb
  sub-directories of 1Mb or more:
    libs  18.6Mb
Error in re-building vignettes:
  ...

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot5d7250e1c985.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5d7250e1c985.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cairoDevice.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Cairo.Rcheck/00install.out’ for details.
makemar : predictions: no visible global function definition for
  ‘rbinom’
mice.impute.rfcat : <anonymous>: no visible global function definition
  for ‘predict’
mice.impute.rfcont: no visible global function definition for ‘predict’
mice.impute.rfcont: no visible global function definition for ‘rnorm’
simdata: no visible global function definition for ‘rbinom’
simdata: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  predict rbinom rnorm
Consider adding
  importFrom("stats", "predict", "rbinom", "rnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CalibrationGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    5.7Mb
    libs   1.7Mb
Package required but not available: ‘aroma.core’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘camel/libs/camel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘SFGen.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘SFGen.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘ncdf4’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-13, (SVN revision 686)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.2-5 
Warning in engine$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 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Packages suggested but not available for checking:
  ‘GenomicRanges’ ‘IRanges’ ‘S4Vectors’
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Error in re-building vignettes:
  ...
Removing 14 individuals due to missing phenotypes.


2 marker(s) rejected due to linear non-independence.
 For more information see markers.removed.for.non.independence.txt
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cape.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Anx1.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \RequirePackage
                    {fancyvrb}^^M
!  ==> 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:
    libs   4.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Using_causaldrf.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'causalsens.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: parallel
Loading required package: pcaPP
Loading required package: robustbase
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ccaPP-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.126 \usepackage
                 {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Error in re-building vignettes:
  ...
If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/

Please cite the 'censReg' package as:
Henningsen, Arne (2017). censReg: Censored Regression (Tobit) Models. R package version 0.5. http://CRAN.R-Project.org/package=censReg.

If you have questions, suggestions, or comments regarding the 'censReg' package, please use a forum or 'tracker' at the R-Forge site of the 'sampleSelection' project:
https://r-forge.r-project.org/projects/sampleselection/
Loading required package: Formula
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'censReg.tex' failed.
LaTeX errors:
! LaTeX Error: File `bbm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘CGManalyzer-Ex.R’ failed
The error most likely occurred in:

> ### Name: MSEbyC.fn
> ### Title: call and run a C program to calculate multiscale entropy
> ### Aliases: MSEbyC.fn
> 
> ### ** Examples
> 
> library(CGManalyzer)
> package.name <- "CGManalyzer"
> source( system.file("SPEC", "SPECexample.R", package = package.name) )
> a <- system.file("SPEC", cFile, package = package.name)
> cFolder0 <- substring(a, 1, nchar(a)-nchar(cFile)-1 )
> cFolder <- gsub("Program Files", "PROGRA~1", cFolder0, fixed = TRUE)
> compileC.fn(cFile=cFile, cFolder=cFolder)
Error in shell(paste0("gcc -o ", cFolder, "/", cmdCore, " -O ", cFolder,  : 
  could not find function "shell"
Calls: compileC.fn
Execution halted
CGPEst: no visible global function definition for ‘dist’
CGPEst : PSI: no visible global function definition for ‘dist’
CGPEst : Stand_PSI: no visible global function definition for ‘dist’
CGPEst : Fop: no visible global function definition for ‘optim’
CGPEst: no visible global function definition for ‘optim’
plotCGP: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("stats", "dist", "optim")
to your NAMESPACE file.
!: no visible global function definition for ‘dev.new’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘setNames’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘slotNames’
lssize : s4gonebyte : fb4: no visible binding for global variable
  ‘slot’
lssize : s4gonebyte : fb4: no visible global function definition for
  ‘object.size’
lssize : s4gone : fs4: no visible global function definition for
  ‘setNames’
lssize : s4gone : fs4: no visible global function definition for
  ‘slotNames’
lssize : s4gone : fs4: no visible binding for global variable ‘slot’
mystat: no visible global function definition for ‘median’
mystat: no visible global function definition for ‘sd’
seqle: no visible global function definition for ‘head’
thekurt: no visible global function definition for ‘var’
theskew: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dev.new head median object.size sd setNames slot slotNames var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("methods", "slot", "slotNames")
  importFrom("stats", "median", "sd", "setNames", "var")
  importFrom("utils", "head", "object.size")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CheddarQuickstart.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    data  59.6Mb
Package suggested but not available for checking: ‘speaq’
Error in re-building vignettes:
  ...
16.42065372042111612.6709691596414
The distribution of the curve data indicates noise. The data should be visually 
inspected with a plot (see examples of diffQ).
Approximate and calculated Tm varri. This is an expected behaviour 

			 but the calculation should be confirmed with a plot (see examples of diffQ).
6.533866827983022021.9375753397427
The Tm calculation (fit, adj. R squared ~ 0.849, NRMSE ~ 0.088) is not optimal presumably
due to noisy data. Check raw melting curve (see examples of diffQ).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'chipPCR.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ComplexHeatmap’
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Error in re-building vignettes:
  ...
R Package to solve regression problems while imposing
	 an L1 constraint on the parameters. Based on S-plus Release 2.1
Copyright (C) 1998, 1999
Justin Lokhorst   <jlokhors@stats.adelaide.edu.au>
Berwin A. Turlach <bturlach@stats.adelaide.edu.au>
Bill Venables     <wvenable@stats.adelaide.edu.au>

Copyright (C) 2002
Martin Maechler <maechler@stat.math.ethz.ch>
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clere.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    extdata  12.4Mb
Package required but not available: ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cloudUtil.tex' failed.
LaTeX errors:
! LaTeX Error: File `pstricks.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/clpAPI.Rcheck/00install.out’ for details.
Missing objects imported by ':::' calls:
  ‘relations:::.make_fit_relation_symdiff_B’
  ‘relations:::fit_relation_LP’ ‘relations:::fit_relation_LP_E_k’
Error in re-building vignettes:
  ...
Loading required package: seriation
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignetteClustered.tex' failed.
LaTeX errors:
! LaTeX Error: File `biblatex.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \bibliography
                 {ClusteredMutationsVignettes.bib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 28 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘moe430a.db’
Package unavailable to check Rd xrefs: ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 \usepackage
                [mathcal]{euscript}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    sd, sigma

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

    is.primitive

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘CGHcall’ ‘CGHregions’ ‘CNVtools’ ‘Biobase’ ‘CGHbase’
Package unavailable to check Rd xrefs: ‘CGHcall’
Errors in running code in vignettes:
when running code in ‘CNVassoc_vignette.Rnw’
  ...
> data(NeveCalled)

> probs <- getProbs(NeveCalled)
Loading required package: CGHbase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘CGHbase’

  When sourcing ‘CNVassoc_vignette.R’:
Error: unable to find required package ‘CGHbase’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: CNVassocData
Loading required package: mixdist
Loading required package: mclust
Package 'mclust' version 5.2.3
Type 'citation("mclust")' for citing this R package in publications.
Loading required package: survival
Loading required package: CGHbase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘CGHbase’

Error: processing vignette 'CNVassoc_vignette.Rnw' failed with diagnostics:
 chunk 40 
Error in .requirePackage(package) : 
  unable to find required package ‘CGHbase’
Execution halted
Package suggested but not available for checking: ‘ridge’
Running examples in ‘codebook-Ex.R’ failed
The error most likely occurred in:

> ### Name: codebook_missingness
> ### Title: Codebook missingness
> ### Aliases: codebook_missingness
> 
> ### ** Examples
> 
> data("bfi")
> codebook_missingness(bfi)
Error in `rownames<-`(`*tmp*`, value = 28L) : 
  attempt to set 'rownames' on an object with no dimensions
Calls: codebook_missingness -> md_pattern -> <Anonymous> -> rownames<-
Execution halted
plot,cold-missing: no visible global function definition for
  ‘extendrange’
Undefined global functions or variables:
  extendrange
Consider adding
  importFrom("grDevices", "extendrange")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/comato.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'R_packages-comf.ltx' failed with diagnostics:
Running 'texi2dvi' on 'R_packages-comf.ltx' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.25 \usepackage
                {multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Package suggested but not available for checking: ‘ConsensusClusterPlus’
Errors in running code in vignettes:
when running code in ‘COMMUNAL.Rnw’
  ...

> BRCA.results <- clusterRange(dataMtx = BRCA.100, ks = ks, 
+     varRange = varRange, validation = measures, verbose = F)
Running COMMUNAL over range of variables...	Loading required package: kohonen
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

  When sourcing ‘COMMUNAL.R’:
Error: invalid argument type
Execution halted
Error in re-building vignettes:
  ...
Loading required package: cluster
Loading required package: clValid
Loading required package: fpc
Loading required package: kohonen
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
The "ward" method has been renamed to "ward.D"; note new "ward.D2"

Error: processing vignette 'COMMUNAL.Rnw' failed with diagnostics:
 chunk 1 
Error in !toroidal : invalid argument type
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'compare-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref} % for \url^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: tcltk

For more information on the usage of the Confidence tool, type:
vignette("confidence")
Examples of input files can be found in:
'/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/confidence.Rcheck/confidence/extdata'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'confidence.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.74 \allsectionsfont
                     {\sffamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Loading required package: SparseM

Attaching package: ‘SparseM’

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

    backsolve

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

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘copula’ ‘vines’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.5Mb
Error in re-building vignettes:
  ...

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

    dbinom, dnorm, dpois, pnorm

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

    cbind, pmax, pmin, rbind

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

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

! Emergency stop.
<read *> 
         
l.79 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘VineCopula’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘CopyNumber450kCancer.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
h.inv: no visible global function definition for ‘pnorm’
h.inv: no visible global function definition for ‘qnorm’
hfunc: no visible global function definition for ‘pnorm’
hfunc: no visible global function definition for ‘qnorm’
modified.cvine.alg: no visible global function definition for ‘qpois’
modified.cvine.alg: no visible global function definition for ‘qnbinom’
modified.cvine.alg: no visible global function definition for ‘cor’
modified.cvine.alg.reg: no visible global function definition for
  ‘qpois’
modified.cvine.alg.reg: no visible global function definition for
  ‘qnbinom’
modified.cvine.alg.reg: no visible global function definition for ‘cor’
rcounts : mysampling: no visible global function definition for ‘runif’
rcounts : mysampling: no visible global function definition for ‘qpois’
rcounts : mysampling: no visible global function definition for
  ‘qnbinom’
rcounts.reg : mysampling: no visible global function definition for
  ‘runif’
rcounts.reg : mysampling: no visible global function definition for
  ‘qpois’
rcounts.reg : mysampling: no visible global function definition for
  ‘qnbinom’
unstructured: no visible global function definition for ‘runif’
Undefined global functions or variables:
  cor pnorm qnbinom qnorm qpois runif
Consider adding
  importFrom("stats", "cor", "pnorm", "qnbinom", "qnorm", "qpois",
             "runif")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/CorrectOverloadedPeaks.Rcheck/00install.out’ for details.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs  17.4Mb
Error in re-building vignettes:
  ...
Loading required package: calibrate
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Correlplot.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

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

    backsolve

The following objects are masked from engel (pos = 3):

    foodexp, income

Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: vignette.aux
I couldn't open style file chicago.bst
---line 45 of file vignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.8Mb
Error in re-building vignettes:
  ...
Loading required package: nlme
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'covBM_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {bm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rmgarch’
Error in re-building vignettes:
  ...
Attaching package: 'fit.models'

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

    mahalanobis

Loading required package: MASS
Loading required package: lattice
Loading required package: robustbase
Loading required package: rrcov
Scalable Robust Estimators with High Breakdown Point (version 1.4-3)

Loading required package: foreach
Loading required package: PerformanceAnalytics

Attaching package: 'PerformanceAnalytics'

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

    legend

Quitting from lines 35-44 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
there is no package called 'rmgarch'
Execution halted
Package suggested but not available for checking: ‘gridGraphics’
Package suggested but not available for checking: ‘qvalue’
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    libs  30.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cplexAPI.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘rgdal’ ‘sf’
Error in re-building vignettes:
  ...

    
ISDA(R) is a registered mark of the International Swaps and
    Derivatives 
Association, Inc.
 
Please type **yes** to assent to
    the aforementioned terms.

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

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(d.lead, alternative = "greater") :
  cannot compute exact p-value with zeroes
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CrossScreening-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {cleveref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    libs  18.5Mb
Running ‘spelling.R’ [9s/9s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [42s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      table
  
  
  [31m──[39m [31m1. Failure: checkInstalledPackages (@test-misc.R#208) [39m [31m──────────────────────[39m
  `checkInstalledPackages(c("not", "installed"))` threw an error with unexpected message.
  Expected match: "Missing required packages: \"not\" and \"installed\""
  Actual message: "Missing required packages: \"installed\""
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2590 SKIPPED: 14 FAILED: 1
  1. Failure: checkInstalledPackages (@test-misc.R#208) 
  
  Error: testthat unit tests failed
  Execution halted
Namespace in Imports field not imported from: ‘yaml’
  All declared Imports should be used.
Missing or unexported object: ‘utils::askYesNo’
Error in re-building vignettes:
  ...
Error: processing vignette 'CryptRndTest.ltx' failed with diagnostics:
Running 'texi2dvi' on 'CryptRndTest.ltx' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
BayesCslogistic: no visible global function definition for
  ‘model.response’
BayesCslogistic: no visible global function definition for
  ‘model.matrix’
MleCslogistic: no visible global function definition for
  ‘model.response’
MleCslogistic: no visible global function definition for ‘model.matrix’
MleCslogistic: no visible global function definition for ‘optim’
plot.BayesCslogistic: no visible global function definition for ‘is’
plot.BayesCslogistic: no visible global function definition for ‘par’
plot.BayesCslogistic: no visible global function definition for
  ‘density’
print.BayesCslogistic: no visible global function definition for ‘coef’
print.MleCslogistic: no visible global function definition for ‘coef’
summary.BayesCslogistic: no visible global function definition for
  ‘var’
summary.BayesCslogistic: no visible global function definition for
  ‘median’
summary.MleCslogistic: no visible global function definition for
  ‘pnorm’
summary.MleCslogistic: no visible global function definition for
  ‘qnorm’
Undefined global functions or variables:
  coef density is median model.matrix model.response optim par pnorm
  qnorm var
Consider adding
  importFrom("graphics", "par")
  importFrom("methods", "is")
  importFrom("stats", "coef", "density", "median", "model.matrix",
             "model.response", "optim", "pnorm", "qnorm", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...

 Lowest minimum so far:  4203.3130332814

Solution found

NPSOL optimizer not available - switching to CSOLNP - consider installing OpenMx using command:  source('http://openmx.psyc.virginia.edu/getOpenMx.R') 
Running ctsem with 19 parameters
Warning in has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Unique discreteDRIFT calculations per step required = 5
Unique discreteCINT calculations per step required = 5
Unique discreteDIFFUSION calculations per step required = 5
2 / 2 latent variables required for covariance calculations
Compiling model, ignore forthcoming warning re number of chains...
the number of chains is less than 1; sampling not done
Sampling...
error occurred during calling the sampler; sampling not done
error occurred during calling the sampler; sampling not done
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
here are whatever error messages were returned
Quitting from lines 294-295 (hierarchical.rnw) 
Error: processing vignette 'hierarchical.rnw' failed with diagnostics:
argument is of length zero
Execution halted
Running examples in ‘CuCubes-Ex.R’ failed
The error most likely occurred in:

> ### Name: ComputeMaxInfoGains
> ### Title: Max information gains
> ### Aliases: ComputeMaxInfoGains
> 
> ### ** Examples
> 
>   ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,
+     discretizations = 1, range = 0, divisions = 22, dimensions = 1)

 *** caught illegal operation ***
address 0x103eaccb1, cause 'illegal opcode'

Traceback:
 1: .C(CuCubes, as.integer(acceleration.type.int), as.integer(0),     as.integer(n), as.integer(k), as.integer(dimensions), as.integer(divisions),     as.integer(discretizations), as.integer(seed), as.double(range),     as.double(pseudo.count), as.integer(reduce.method.int), as.double(0),     integer(length = 0), as.integer(0), as.double(data), as.integer(decision),     out = double(length = k))
 2: ComputeMaxInfoGains(data = madelon$data, decision = madelon$decision,     discretizations = 1, range = 0, divisions = 22, dimensions = 1)
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/cudaBayesreg.Rcheck/00install.out’ for details.
Packages unavailable to check Rd xrefs: ‘DNAcopy’, ‘tilingArray’
path.plot: no visible global function definition for ‘plot’
path.plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot
Consider adding
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChangeLogcwhmisc.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `russian'. Either you misspelled it
(babel)                or the language definition file russian.ldf was not foun
d.

See the babel package documentation for explanation.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'presentazioneCladagMinottiSpedicato.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Sparseness = 75.35 %
  Sorting covariates by covariateId and rowId
  ── 1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R
  `loadNewSeqlCyclopsDataMultipleX(dataPtr, c(1, 1), c(1, 1), NULL)` threw an error with unexpected message.
  Expected match: "1 - 1"
  Actual message: "c++ exception (unknown reason)"
  
  Sparseness = 99.09 %
  Sorting covariates by covariateId and rowId
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 201 SKIPPED: 17 FAILED: 1
  1. Failure: Data errors and casting in COO-constructor (@test-xyConstructor.R#212) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object ''
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error: processing vignette 'marray-notes.Rnw' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simulate-regdiags.tex' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

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

! Emergency stop.
<read *> 
         
l.1 ...ohyper,justified]{tufte-handout}\usepackage
                                                  []{graphicx}\usepackage[]{...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/DAC.Rcheck/00install.out’ for details.
y.stand: no visible binding for global variable ‘sd’
Undefined global functions or variables:
  sd
Consider adding
  importFrom("stats", "sd")
to your NAMESPACE file.
Package unavailable to check Rd xrefs: ‘gputools’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot146936df7e8db.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot146936df7e8db.png': No such file or directory
Quitting from lines 61-72 (dataexplorer-intro.Rmd) 
Error: processing vignette 'dataexplorer-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 55.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  52.9Mb
Error in re-building vignettes:
  ...
Warning in engine$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 78-85 (Introduction_to_datasus.Rmd) 
Error: processing vignette 'Introduction_to_datasus.Rmd' failed with diagnostics:
Timeout was reached: Connection timed out after 10010 milliseconds
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.
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]="./webshot7855792c4f41.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot7855792c4f41.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Package required but not available: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Note: found 83 marked Latin-1 strings
  Note: found 62 marked UTF-8 strings
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Note due to namespace conflicts between MASS and trafficlight this package will not work if trafficlight is loaded
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UserGuide.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.54 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘WGCNA’
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.4Mb
    libs   1.5Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'desirability.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘Rmosek’ ‘gurobi’
Package unavailable to check Rd xrefs: ‘Rmosek’
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
Namespaces in Imports field not imported from:
  ‘Cairo’ ‘sparkline’
  All declared Imports should be used.
Unexported objects imported by ':::' calls:
  ‘dexter:::get_resp_data’ ‘dexter:::qcolors’
  See the note in ?`:::` about the use of this operator.
installed size is 45.4Mb
  sub-directories of 1Mb or more:
    libs  45.0Mb
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   8.9Mb
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Rvignette_DiagTest3Grp.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
beadsplot.formula: no visible global function definition for
  ‘model.frame’
calc.stats: no visible global function definition for ‘str’
do.call.with.par: no visible global function definition for
  ‘modifyList’
make.colors: no visible global function definition for ‘rainbow’
make.colors : <anonymous>: no visible global function definition for
  ‘adjustcolor’
make.scale: no visible global function definition for ‘modifyList’
only.graphic.pars: no visible global function definition for ‘par’
plt.diamond: no visible global function definition for ‘polygon’
plt.diamond: no visible global function definition for ‘lines’
plt.gridline: no visible global function definition for ‘abline’
plt.gridline: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  abline adjustcolor lines model.frame modifyList mtext par polygon
  rainbow str
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "abline", "lines", "mtext", "par", "polygon")
  importFrom("stats", "model.frame")
  importFrom("utils", "modifyList", "str")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/diffMeanVar.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Sampling sensitivity with m=500 gamma=0.2 k=439
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bernstein.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {amsfonts}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error in re-building vignettes:
  ...
  not all rows sum up to 1 => normalization forced
Warning in DR_data(Bld[31:36, 1:4]) :
  not all rows sum up to 1 => normalization forced
Warning in DR_data(Bld[31:36, 1:4]) :
  not all rows sum up to 1 => normalization forced
Warning in DR_data(BloodSamples[, c(1, 2, 4)]) :
  not all rows sum up to 1 => normalization forced
only one variable in [0, 1] supplied - beta-distribution assumed.
check this assumption.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DirichletReg-vig.tex' failed.
LaTeX errors:
! LaTeX Error: File `blkarray.sty' not found.

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

! Emergency stop.
<read *> 
         
l.50 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dirmcmc_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
DiscML : midpoint : allAncestors: no visible global function definition
  for ‘reorder’
DiscML : midpoint : reroot: no visible global function definition for
  ‘reorder’
DiscML : midpoint : node2root: no visible global function definition
  for ‘reorder’
DiscML : midpoint: no visible global function definition for ‘reorder’
DiscML: no visible global function definition for ‘reorder’
DiscML : DiscML2 : dev: no visible global function definition for
  ‘qgamma’
DiscML : DiscML2 : dev: no visible global function definition for ‘is’
DiscML : DiscML2: no visible global function definition for ‘nlminb’
DiscML : DiscML2: no visible global function definition for ‘nlm’
DiscML: no visible global function definition for ‘par’
DiscML: no visible global function definition for ‘plot’
DiscML: no visible global function definition for ‘axis’
DiscML: no visible global function definition for ‘axTicks’
DiscML: no visible global function definition for ‘text’
Undefined global functions or variables:
  axTicks axis is nlm nlminb par plot qgamma reorder text
Consider adding
  importFrom("graphics", "axTicks", "axis", "par", "plot", "text")
  importFrom("methods", "is")
  importFrom("stats", "nlm", "nlminb", "qgamma", "reorder")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Package unavailable to check Rd xrefs: ‘diversitree’
Error in re-building vignettes:
  ...
Cross tabulating interactions for gbm model with 11 predictors
1 2 3 4 5 6 7 8 9 10 
maximum value = 0.58

Loading required package: survival
Loading required package: lattice
Loading required package: splines
Loading required package: parallel
Loaded gbm 2.1.3
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'brt.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
distfree.cr: no visible global function definition for ‘plot’
linescrosspoint: no visible global function definition for ‘na.exclude’
plot.distfree.cr: no visible global function definition for ‘plot’
plot.distfree.cr: no visible global function definition for ‘points’
plot.distfree.cr: no visible global function definition for ‘polygon’
plot.distfree.cr: no visible global function definition for ‘legend’
xy.quantile: no visible global function definition for ‘quantile’
Undefined global functions or variables:
  legend na.exclude plot points polygon quantile
Consider adding
  importFrom("graphics", "legend", "plot", "points", "polygon")
  importFrom("stats", "na.exclude", "quantile")
to your NAMESPACE file.
Package suggested but not available for checking: ‘Biobase’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'diveRsity.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DNAtools.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘copula’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doRedis.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.22 \usepackage
                {upquote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘doMPI’ ‘devtools’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doRNG-unitTests.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \setmargrb
               {0.75in}{0.75in}{0.75in}{0.75in}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Downscaling.tex' failed.
LaTeX errors:
! LaTeX Error: File `silence.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Namespaces in Imports field not imported from:
  ‘bit64’ ‘rstudioapi’ ‘tidyverse’
  All declared Imports should be used.
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘readr’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
                        sleep dataset
presidential            Terms of 11 presidents from Eisenhower to Obama
seals                   Vector field of seal movements
txhousing               Housing sales in TX


Use ‘data(package = .packages(all.available = TRUE))’
to list the data sets in all *available* packages.

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

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   4.0Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  13.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svminternals.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Namespaces in Imports field not imported from:
  ‘corrplot’ ‘scorer’
  All declared Imports should be used.
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: EasyMx-package
> ### Title: EasyMx: Easy modeling in OpenMx
> ### Aliases: EasyMx-package EasyMx
> 
> ### ** Examples
> 
> 
> # Make and run a one factor model
> require(EasyMx)
> 
> data(demoOneFactor)
> fmod <- list(G=names(demoOneFactor))
> fit1 <- emxFactorModel(fmod, demoOneFactor, run=TRUE)
Error: The row names of the LX matrix and the row names of the TX matrix in model 'Model' do not contain identical names.
Execution halted
File ‘EBS/libs/EBS.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘untb’
Package suggested but not available for checking: ‘cheddar’
Running examples in ‘econullnetr-Ex.R’ failed
The error most likely occurred in:

> ### Name: generate_edgelist
> ### Title: Export null modelling results
> ### Aliases: generate_edgelist
> 
> ### ** Examples
> 
> set.seed(1234)
> bs.null <- generate_null_net(Broadstone, Broadstone.prey, data.type = "counts",
+                              sims = 10, r.weights = Broadstone.fl)
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
> BS.export <- generate_edgelist(bs.null, signif.level = 0.95)
> 
> # Plot network with functions from the cheddar package
> library(cheddar)
Error in library(cheddar) : there is no package called ‘cheddar’
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 bipartite::plotweb(obs.web, method = "normal", empty = FALSE,  :
  interaction width is influenced by abundance vector and possibly not proportional to link weight
Quitting from lines 247-261 (econullnetr-intro.Rmd) 
Error: processing vignette 'econullnetr-intro.Rmd' failed with diagnostics:
there is no package called 'cheddar'
Execution halted
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ecr.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Running examples in ‘edmcr-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeA
> ### Title: Create Molecule Metadata
> ### Aliases: makeA
> 
> ### ** Examples
> 
> A <- makeA()
Warning in file(file, "rt") :
  cannot open file '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/edmcr.Rcheck/edmcr/extdata/AMatrix/atom\name\A1atom_name1.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: makeA -> read.table -> file
Execution halted
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
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.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EGRET.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.66 \usepackage
                {subfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you want to change this use: options(tv_home="<path_to_your_Turbowin_root>")
############################################################
Some columns contain no data and are omitted.
Some numeric columns contain only 0 values and are omitted.
Some numeric fields contain 0 values:
Please check if these are really meant as 0 or if they are erroneously assigned because of DBase restrictions.
If so, use something like:
site$Column_name[site$Column_name==0] <- NA

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'eHOF.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: eiPack
Loading required package: MASS
Loading required package: coda
Loading required package: msm
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ei.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.22 \usepackage
                {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ElastH.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
anellipse: no visible global function definition for ‘str’
anellipse: no visible global function definition for ‘polygon’
ellipseplot.data.frame: no visible global function definition for ‘par’
ellipseplot.default: no visible global function definition for ‘par’
ellipses: no visible global function definition for ‘text’
ellipses: no visible global function definition for ‘mtext’
many.ellipses: no visible global function definition for ‘modifyList’
many.ellipses: no visible global function definition for ‘hasArg’
many.ellipses: no visible global function definition for ‘rainbow’
sheer.color: no visible global function definition for ‘adjustcolor’
Undefined global functions or variables:
  adjustcolor hasArg modifyList mtext par polygon rainbow str text
Consider adding
  importFrom("grDevices", "adjustcolor", "rainbow")
  importFrom("graphics", "mtext", "par", "polygon", "text")
  importFrom("methods", "hasArg")
  importFrom("utils", "modifyList", "str")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Error in re-building vignettes:
  ...
    sd, sigma

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

    is.primitive

Loading required package: emulator
Loading required package: mvtnorm
Loading required package: calibrator
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ellipticpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tutorial.tex' failed.
BibTeX errors:
The top-level auxiliary file: tutorial.aux
I couldn't open style file agsm.bst
---line 3 of file tutorial.aux
 : \bibstyle{agsm
 :               }
I'm skipping whatever remains of this command
I found no style file---while reading file tutorial.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: ElstonStewart
Loading required package: kinship2
Loading required package: Matrix
Loading required package: quadprog
Loading required package: parallel
Loading required package: digest
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Elston-Stewart.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘GO.db’
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/emil.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   7.5Mb
Running ‘testthat.R’ [57s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  18: as(set_TextType(methods_file), "description")
  19: .class1(object)
  20: set_TextType(methods_file)
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 76 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
wire.init.fit : wire.init.km: no visible global function definition for
  ‘kmeans’
wire.init.reg: no visible global function definition for ‘lm’
wire.init.reg: no visible global function definition for ‘coef’
wire.init.reg: no visible global function definition for ‘resid’
Undefined global functions or variables:
  coef kmeans lm resid
Consider adding
  importFrom("stats", "coef", "kmeans", "lm", "resid")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ggtree’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
'showtext.begin()' is now renamed to 'showtext_begin()'
The old version still works, but consider using the new function in future code
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
there is no package called 'ggtree'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘spocc’ ‘rgeos’
Error in re-building vignettes:
  ...
ERROR: dependency ‘rgeos’ is not available for package ‘geoaxe’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/geoaxe’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'geoaxe' had non-zero exit status
ERROR: dependency ‘geoaxe’ is not available for package ‘rgbif’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/rgbif’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'rgbif' had non-zero exit status
ERROR: dependency ‘rgbif’ is not available for package ‘spocc’
* removing ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ENMeval.Rcheck/spocc’
Warning in install.packages("spocc", repos = "http://cran.us.r-project.org") :
  installation of package 'spocc' had non-zero exit status

The downloaded source packages are in
	'/private/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T/Rtmpf3RLJr/downloaded_packages'
Loading required package: ENMeval
Loading required package: dismo
Loading required package: raster
Loading required package: sp
Loading required package: rJava
Loading required package: parallel
Quitting from lines 38-52 (ENMeval-vignette.Rmd) 
Error: processing vignette 'ENMeval-vignette.Rmd' failed with diagnostics:
there is no package called 'spocc'
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    Sweave   6.0Mb
Packages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘MSnbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: survival
Package epiR 0.9-79 is loaded
Type help(epi.about) for summary information


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'EpiBayes2Level.tex' failed.
LaTeX errors:
! LaTeX Error: File `titling.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {datetime}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot19815cfbc06b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19815cfbc06b.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘readr’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/epubr.Rcheck/00install.out’ for details.
eqs2lavaan: no visible binding for global variable ‘r’
eqsCorr: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘cov2cor’
plotCov: no visible global function definition for ‘par’
plotCov: no visible global function definition for ‘image’
plotCov: no visible global function definition for ‘axis’
Undefined global functions or variables:
  axis cov2cor image par r
Consider adding
  importFrom("graphics", "axis", "image", "par")
  importFrom("stats", "cov2cor")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Optimizing with step length 1.
The log-likelihood improved by 0.01689.
Step length converged once. Increasing MCMC sample size.
Iteration 2 of at most 20:
Optimizing with step length 1.
The log-likelihood improved by 0.003609.
Step length converged twice. Stopping.
Evaluating log-likelihood at the estimate. Using 20 bridges: 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 .
This model was fit using MCMC.  To examine model diagnostics and check for degeneracy, use the mcmc.diagnostics() function.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ergm.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘graph’
Errors in running code in vignettes:
when running code in ‘ESEA.Rnw’
  ...

> PathwayNetwork <- Results[[2]][[1]]

> SavePathway2File(PathwayNetwork, layout = layout.circle, 
+     file = "Graph")
[1] "...writing to file"

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

Attaching package: ‘igraph’

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

    decompose, spectrum

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

    union

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: parmigene

Error: processing vignette 'ESEA.Rnw' failed with diagnostics:
 chunk 11 
Error in loadNamespace(name) : there is no package called ‘graph’
Execution halted
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
avec.cov: no visible global function definition for ‘qnorm’
closPseudo: no visible global function definition for ‘terms’
etmCIF: no visible global function definition for ‘model.extract’
lines.etm: no visible global function definition for ‘lines’
phiPseudo: no visible global function definition for ‘terms’
plot.clos.etm: no visible global function definition for ‘par’
plot.clos.etm: no visible global function definition for ‘split.screen’
plot.clos.etm: no visible global function definition for ‘screen’
plot.clos.etm: no visible global function definition for ‘plot’
plot.clos.etm: no visible global function definition for ‘axis’
plot.clos.etm: no visible global function definition for ‘box’
plot.clos.etm: no visible global function definition for ‘lines’
plot.clos.etm: no visible global function definition for ‘close.screen’
plot.etm: no visible global function definition for ‘plot’
plot.etm: no visible global function definition for ‘lines’
plot.etmCIF: no visible global function definition for ‘plot’
plot.etmCIF: no visible global function definition for ‘lines’
plot.etmCIF: no visible global function definition for ‘segments’
print.summary.etm: no visible global function definition for ‘quantile’
print.summary.etmCIF: no visible global function definition for
  ‘quantile’
Undefined global functions or variables:
  axis box close.screen lines model.extract par plot qnorm quantile
  screen segments split.screen terms
Consider adding
  importFrom("graphics", "axis", "box", "close.screen", "lines", "par",
             "plot", "screen", "segments", "split.screen")
  importFrom("stats", "model.extract", "qnorm", "quantile", "terms")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Unknown package ‘DNAprofiles’ in Rd xrefs
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'events.tex' failed.
LaTeX errors:
! LaTeX Error: File `mathdesign.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {inconsolata}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'replications.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \usepackage
                [colorlinks,linkcolor=blue,citecolor=red]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘exams-Ex.R’ failed
The error most likely occurred in:

> ### Name: exams2openolat
> ### Title: Generation of Exams for OpenOLAT
> ### Aliases: exams2openolat
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## define an exams (= list of exercises)
> myexam <- list(
+   "boxplots",
+   c("tstat", "ttest", "confint"),
+   c("regression", "anova"),
+   c("scatterplot", "boxhist"),
+   "relfreq"
+ )
> 
> ## output directory
> mydir <- tempdir()
> 
> ## generate .zip with OpenOLAT test in temporary directory
> exams2openolat(myexam, n = 3, dir = mydir)
Loading required namespace: rmarkdown
sh: +RTS: command not found
Error: pandoc document conversion failed with error 127
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/excerptr.Rcheck/00install.out’ for details.
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    exiftool  12.3Mb
'library' or 'require' call to ‘fields’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘parallel’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
The following objects are masked from ‘package:foreign’:

    read.dbf, write.dbf

Note: Function plotsurf depends on akima which has
 a restricted licence that explicitly forbids commercial use.
 akima is therefore disabled by default and may be enabled by
 akimaPermit(). Calling this function includes your agreement to
 akima`s licence restrictions.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'expectreg.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘Rmpfr’
Error in re-building vignettes:
  ...
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Warning: The labeller API has been updated. Labellers taking `variable`and `value` arguments are now deprecated. See labellers documentation.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FAOSTAT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {draftwatermark}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.2Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Error in re-building vignettes:
  ...


Attaching package: 'fastR'

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

    panel.smooth

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

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   1.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
installed size is 35.1Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.3Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.2Mb
Error in re-building vignettes:
  ...

Attaching package: ‘fdth’

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

    sd, var

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

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {multirow}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test-as-dgCMatrix.R’ [2s/2s]
  Running ‘test-empty_array.R’ [3s/3s]
  Running ‘test-existence_collision.R’ [2s/2s]
  Running ‘test-hash.mapping.R’ [2s/2s]
  Running ‘test-hashing.R’ [2s/2s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ffstream.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'testTimeAndSimpleUse.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro-fgpt.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \makeatletter
                  ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: fifer
Loading required package: MASS
Loading required package: xtable
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'fifer_package.tex' failed.
LaTeX errors:
! LaTeX Error: File `apa.cls' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {hyperref}  %this allows us to cite URLs in the text^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gb2016_complement.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' calls in package code:
  ‘e1071’ ‘fUnitRoots’ ‘polynom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘examples/fitcoach-usage.Rmd’, ‘examples/fitcoach-usage.html’,
    ‘summary.Rmd’, ‘summary.html’
Package has no Sweave vignette sources and no VignetteBuilder field.
plot.fkf: no visible global function definition for ‘rainbow’
plot.fkf: no visible global function definition for ‘qnorm’
plot.fkf: no visible global function definition for ‘qqnorm’
plot.fkf: no visible global function definition for ‘qchisq’
plot.fkf: no visible global function definition for ‘ppoints’
plot.fkf: no visible global function definition for ‘qqplot’
plot.fkf: no visible global function definition for ‘acf’
plot.fkf: no visible global function definition for ‘ccf’
Undefined global functions or variables:
  acf ccf ppoints qchisq qnorm qqnorm qqplot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("stats", "acf", "ccf", "ppoints", "qchisq", "qnorm",
             "qqnorm", "qqplot")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘devtools’ ‘multipanelfigure’
Package suggested but not available for checking: ‘limma’
Error in re-building vignettes:
  ...
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ClassDiagram.tex' failed.
LaTeX errors:
! LaTeX Error: File `pbox.sty' not found.

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

! Emergency stop.
<read *> 
         
l.56 \usepackage
                {adjustbox}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘methods’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
AIC.freekt: no visible global function definition for ‘residuals’
AICc.freekt: no visible global function definition for ‘residuals’
BIC.freekt: no visible global function definition for ‘residuals’
adjAIC.freekt: no visible global function definition for ‘residuals’
adjGCV.freekt: no visible global function definition for ‘residuals’
chgbasismat: no visible global function definition for ‘splineDesign’
coef.freekt: no visible global function definition for ‘splineDesign’
fit.search.numknots: no visible global function definition for ‘AIC’
fit.search.numknots: no visible global function definition for ‘BIC’
fitted.freekt: no visible global function definition for ‘splineDesign’
freelsgen: no visible global function definition for ‘new’
freelsgold: no visible global function definition for ‘new’
freepsgen: no visible global function definition for ‘new’
freepsgold: no visible global function definition for ‘new’
plot.freekt: no visible global function definition for ‘plot’
plot.freekt: no visible global function definition for ‘lines’
summary.freekt: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  AIC BIC lines new plot residuals splineDesign
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("methods", "new")
  importFrom("stats", "AIC", "BIC", "residuals")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
Error in re-building vignettes:
  ...
Iacus, Springer NY, (2008)
To check the errata corrige of the book, type vignette("sde.errata")

Attaching package: ‘ftsa’

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

    sd, var

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

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘WGCNA’
Package unavailable to check Rd xrefs: ‘cffdrs’
Error in re-building vignettes:
  ...

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

    as.Date, as.Date.numeric

Loading required package: strucchange
Loading required package: sandwich
Warning in sub(object$syntax$docexpr, val, chunk[pos[1L]]) :
  argument 'replacement' has length > 1 and only the first element will be used
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
GA4StratificationP1: no visible global function definition for
  ‘flush.console’
GA4StratificationP1m: no visible global function definition for ‘runif’
GA4StratificationP2: no visible global function definition for
  ‘flush.console’
GA4StratificationP2m: no visible global function definition for ‘runif’
GA4StratificationP3: no visible global function definition for
  ‘flush.console’
GA4StratificationP3m: no visible global function definition for ‘runif’
GA4StratificationP4: no visible global function definition for ‘runif’
GA4StratificationP4: no visible global function definition for
  ‘flush.console’
GA4StratificationP4m: no visible global function definition for ‘runif’
GA4StratificationSelection: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  flush.console runif
Consider adding
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
Package suggested but not available for checking: ‘ArrayBin’
Error in re-building vignettes:
  ...


Attaching package: 'gamboostLSS'

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

    model.weights

Loading required namespace: BayesX
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gamboostLSS_Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Unexported object imported by a ':::' call: ‘gamlss:::numeric.deriv’
  See the note in ?`:::` about the use of this operator.
Error in re-building vignettes:
  ...
Loading required package: gamlss.data
Loading required package: gamlss.dist
Loading required package: MASS
Loading required package: nlme
Loading required package: parallel
 **********   GAMLSS Version 5.0-1  ********** 
For more on GAMLSS look at http://www.gamlss.org/
Type gamlssNews() to see new features/changes/bug fixes.

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

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

! Emergency stop.
<read *> 
         
l.55 \usepackage
                {Rd}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.8Mb
installed size is 60.3Mb
  sub-directories of 1Mb or more:
    libs  59.9Mb
installed size is 48.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     45.3Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  12.8Mb
Error in .requirePackage(package) : 
    unable to find required package 'raster'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: g.data
Warning in g.data.attach(ddp) :
  New DDP: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpTHh796/newdir154642e4489b6
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'g.data.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {indentfirst}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error in re-building vignettes:
  ...
Loading required package: geepack
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'geepack-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gems.tex' failed.
LaTeX errors:
! LaTeX Error: File `pict2e.sty' not found.

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

! Emergency stop.
<read *> 
         
l.81 \usepackage
                {tikz}^^M
!  ==> 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:
    java   5.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.5Mb
Package suggested but not available for checking: ‘snpStats’
Package unavailable to check Rd xrefs: ‘snpStats’
Error in .requirePackage(package) : 
    unable to find required package 'snpStats'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Running examples in ‘GenCAT-Ex.R’ failed
The error most likely occurred in:

> ### Name: GenCAT
> ### Title: Running GenCAT
> ### Aliases: GenCAT
> ### Keywords: ~kwd1 ~kwd2
> 
> ### ** Examples
> 
> 
> ###############
> #Running GenCAT
> ###############
> data("CardioMapped")
> 
> #Subset CardioMapped to decrease CPU time
> CardioMappedSub<-CardioMapped[CardioMapped$chr < 15,]
> set.seed(1)
> CardioMappedSub<-CardioMappedSub[sample(1:nrow(CardioMappedSub), 100),]
> 
> print(head(CardioMappedSub))
            SNP effect_allele other_allele   testStat chr position class
17232 rs9572807             C            T -0.3014771  13 72423959 DACH1
24151 rs4389009             G            A -1.4443860  13 99193519 STK24
37178 rs7151730             T            A  0.1387317  14 33531585 NPAS3
58941 rs1076958             G            A  2.0597766  14 91131857 TTC7B
13089 rs7987481             G            A -1.0024210  13 47318950 LRCH1
58302  rs411064             G            A  0.2132412  14 90008860 FOXN3
> 
> library(snpStats)
Error in library(snpStats) : there is no package called ‘snpStats’
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
Loading required package: ggplot2
Quitting from lines 62-69 (GenCAT-vignette.Rmd) 
Error: processing vignette 'GenCAT-vignette.Rmd' failed with diagnostics:
unable to find required package 'snpStats'
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Geneland-Doc.pdf’, ‘Geneland-Doc.tex’, ‘dag-final.pdf’, ‘dag3.pdf’,
    ‘fig/MCMC.jpg’, ‘fig/MyMap_zoom10.jpeg’, ‘fig/MyMap_zoom7.jpeg’,
    ‘fig/choosefiles.jpg’, ‘fig/choosesep.jpg’, ‘fig/dag-final.pdf_t’,
    ‘fig/dag3.pdf_t’, ‘fig/example_spatial2_bis.jpeg’,
    ‘fig/example_spatial3_bis.jpeg’, ‘fig/example_spatial3_ter.jpeg’,
    ‘fig/example_spatial_bis.jpeg’, ‘fig/exp_q_quart.jpeg’,
    ‘fig/initial.jpg’, ‘fig/map.jpeg’, ‘fig/multip_run.jpg’,
    ‘fig/multip_run2.jpg’, ‘fig/npop.jpeg’, ‘fig/output.jpg’,
    ‘fig/parallel.jpg’, ‘fig/postproc.jpg’, ‘fig/power.jpeg’,
    ‘fig/vor1.jpeg’, ‘fig/vor2.jpeg’, ‘fig/wdl1.jpeg’
Package has no Sweave vignette sources and no VignetteBuilder field.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...

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

    decompose, spectrum

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

    union

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Packages suggested but not available for checking:
  ‘KEGG.db’ ‘reactome.db’ ‘AnnotationDbi’
Error in re-building vignettes:
  ...
Warning: namespace ‘evaluate’ is not available and has been replaced
by .GlobalEnv when processing object ‘’
Warning: namespace 'evaluate' is not available and has been replaced
by .GlobalEnv when processing object 'force_v1'
Error: processing vignette 'geoaxe_vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.9Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Error in re-building vignettes:
  ...
A Package for Generalised Linear Spatial Models


geoRglm version 0.9-11 (2017-10-17) is now loaded

-----------------------------------------------------------



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

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

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/geotoolsR.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Namespaces in Imports field not imported from:
  ‘dplyr’ ‘ggmap’ ‘gridExtra’ ‘scales’ ‘tnet’
  All declared Imports should be used.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ggdistribute.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Error in re-building vignettes:
  ...
  conversion failure on 'Barbara Choroś-Tomczyk' in 'mbcsToSbcs': dot substituted for <9b>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <c5>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <99>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <c5>
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  conversion failure on 'Ondřej Chochola' in 'mbcsToSbcs': dot substituted for <99>
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ggenealogy.tex' failed.
LaTeX errors:
! LaTeX Error: File `media9.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required and available but unsuitable version: ‘rvcheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
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]="./webshot1243b62c4d438.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1243b62c4d438.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ggplotgui.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Running examples in ‘ggsn-Ex.R’ failed
The error most likely occurred in:

> ### Name: blank
> ### Title: Blank theme
> ### Aliases: blank
> 
> ### ** Examples
> 
> library(rgdal)
Error in library(rgdal) : there is no package called ‘rgdal’
Execution halted
Package suggested but not available for checking: ‘vdiffr’
Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  testthat results ================================================================
  OK: 15 SKIPPED: 0 FAILED: 13
  1. Error: geom_linerangeh() flips (@test-geoms.R#7) 
  2. Error: geom_pointangeh() flips (@test-geoms.R#13) 
  3. Error: geom_crossbarh() flips (@test-geoms.R#31) 
  4. Error: geom_errorbarh() flips (@test-geoms.R#37) 
  5. Error: geom_barh() flips (@test-geoms.R#45) 
  6. Error: geom_histogramh() flips (@test-geoms.R#57) 
  7. Error: geom_violinh() flips (@test-geoms.R#71) 
  8. Error: geom_boxploth() flips (@test-geoms.R#81) 
  9. Error: facet_grid() with free scales flips (@test-geoms.R#95) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...

Warning in (psi + skewness.norm) * (chi + Q) :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in log.const.top + log.top :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Generalized_Hyperbolic_Distribution.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GlobalAncova’ ‘globaltest’ ‘limma’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘GlobalAncova’, ‘globaltest’, ‘DESeq’, ‘limma’
Running examples in ‘GiANT-Ex.R’ failed
The error most likely occurred in:

> ### Name: GiANT-package
> ### Title: Enrichment analysis
> ### Aliases: GiANT
> 
> ### ** Examples
> 
> # load data
> require(GlobalAncova)
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GlobalAncova’
> data(vantVeer)
Warning in data(vantVeer) : data set ‘vantVeer’ not found
> data(phenodata)
Warning in data(phenodata) : data set ‘phenodata’ not found
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found
> 
> ##################################
> # Example 1: gene set analysis   #
> ##################################
> res <- geneSetAnalysis(  
+   # parameters for geneSetAnalysis
+   dat = vantVeer,
+   geneSets = pathways[1:3],
+   analysis = analysis.averageCorrelation(),
+   adjustmentMethod = "fdr",
+   # additional parameters for analysis.averageCorrelation
+   labs = phenodata$metastases,
+   method = "pearson",
+   numSamples = 100)
Error in vector(mode = "list", length = length(geneSets)) : 
  object 'pathways' not found
Calls: geneSetAnalysis -> vector
Execution halted
Errors in running code in vignettes:
when running code in ‘giant_package_vignette.Snw’
  ...
> data(pathways)
Warning in data(pathways) : data set ‘pathways’ not found

> resGsea <- geneSetAnalysis(labs = phenodata$metastases, 
+     method = "pearson", numSamples = 1000, dat = vantVeer, geneSets = pathways, 
+     an .... [TRUNCATED] 

  When sourcing ‘giant_package_vignette.R’:
Error: object 'pathways' not found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: GlobalAncova
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GlobalAncova’
Warning in data(vantVeer) : data set ‘vantVeer’ not found
Warning in data(phenodata) : data set ‘phenodata’ not found
Warning in data(pathways) : data set ‘pathways’ not found

Error: processing vignette 'giant_package_vignette.Snw' failed with diagnostics:
 chunk 5 
Error in vector(mode = "list", length = length(geneSets)) : 
  object 'pathways' not found
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GiRaF_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘BSgenome.Hsapiens.UCSC.hg18.masked’
  ‘BSgenome.Hsapiens.UCSC.hg19.masked’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
fitgl: no visible global function definition for ‘na.omit’
fitgl: no visible global function definition for ‘median’
fitgl: no visible global function definition for ‘IQR’
fitgl: no visible binding for global variable ‘hist’
fitgl: no visible global function definition for ‘ppoints’
fitgl: no visible global function definition for ‘quantile’
fitgl: no visible global function definition for ‘nlminb’
glshapeplot: no visible global function definition for ‘plot’
glshapeplot: no visible global function definition for ‘title’
glshapeplot : momentLine: no visible global function definition for
  ‘lines’
glshapeplot: no visible global function definition for ‘points’
Undefined global functions or variables:
  IQR hist lines median na.omit nlminb plot points ppoints quantile
  title
Consider adding
  importFrom("graphics", "hist", "lines", "plot", "points", "title")
  importFrom("stats", "IQR", "median", "na.omit", "nlminb", "ppoints",
             "quantile")
to your NAMESPACE file.
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  39.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/glm2.Rcheck/00install.out’ for details.
installed size is 39.8Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
installed size is 58.4Mb
  sub-directories of 1Mb or more:
    libs  57.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/glpkAPI.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘preprocessCore’
Running examples in ‘glycanr-Ex.R’ failed
The error most likely occurred in:

> ### Name: quantilenorm
> ### Title: Quantile Normalization of glycan data
> ### Aliases: quantilenorm
> 
> ### ** Examples
> 
> data(mpiu)
> mpiun <- quantilenorm(mpiu)
Error in quantilenorm(mpiu) : 
  Unable to proceed since package preprocessCore from
        BioConductor is not available on this system. This
        package is a prerequisite to use the quantilenorm function!
Execution halted
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Error in quantilenorm(mpiu, transpose = TRUE) : 
    Unable to proceed since package preprocessCore from
          BioConductor is not available on this system. This
          package is a prerequisite to use the quantilenorm function!
  Calls: test_check ... force -> source_file -> eval -> eval -> quantilenorm
  testthat results ================================================================
  OK: 5 SKIPPED: 0 FAILED: 0
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gmatrix.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:base':

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

trying URL 'http://i.space.com/images/i/000/010/634/original/shuttle-atlantis-lifts-off.jpg?1309297321'
Content type 'image/jpeg' length 776635 bytes (758 KB)
==================================================
downloaded 758 KB

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

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

! Emergency stop.
<read *> 
         
l.117 ^^M
         
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
that memeber histograms have the same order of the bins.

Warning in as.mhist(tmp.x) :
  `bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.

Warning in as.mhist(tmp.x) :
  `bins' are not specified; use automatic numbering instead under assumption
that memeber histograms have the same order of the bins.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'GMD-data-processing.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘Rmpfr’
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘imudata’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Error in re-building vignettes:
  ...

Warning in Delta1_xk * mystep :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in Delta1_xk * mystep :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

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

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

! Emergency stop.
<read *> 
         
l.43 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

Warning in setCoefs - ref %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in setCoefs - scaleRef %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in setCoefs - ref %*% setCoefs :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gnmOverview.tex' failed.
BibTeX errors:
The top-level auxiliary file: gnmOverview.aux
I couldn't open style file chicago.bst
---line 181 of file gnmOverview.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file gnmOverview.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘copula’ ‘VineCopula’

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

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gPCA.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {bm} % allows for bold math symbols^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gpHist.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

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

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

! Emergency stop.
<read *> 
         
l.21 \usepackage
                [colorlinks,bookmarks,bookmarksopen=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning in glm(as.formula(paste(Y.name, "~ ", paste(indicators_tree[-nber_indicators],  :
  fitting to calculate the null deviance did not converge -- increase 'maxit'?
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `chicago.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [colorlinks = true, linkcolor = blue, breaklinks, citecolor =...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/gputools.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ge-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘gRapHD-Ex.R’ failed
The error most likely occurred in:

> ### Name: modelFormula
> ### Title: Model's formula
> ### Aliases: modelFormula
> ### Keywords: graphs
> 
> ### ** Examples
> 
> data(dsMixed)
> m <- minForest(dsMixed,homog=TRUE,stat="LR")
> modelFormula(m)

 *** caught segfault ***
address 0x0, cause 'memory not mapped'

Traceback:
 1: perfSets(edges = edgesV, p = n, varType = varType, from = 0)
 2: psSub(edges, p, discr, varType[discr])
 3: modelFormula(m)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'manual_de.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `greek'. Either you misspelled it
(babel)                or the language definition file greek.ldf was not found.


See the babel package documentation for explanation.
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8x]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Packages suggested but not available for checking: ‘devtools’ ‘rgdal’
Running examples in ‘graticule-Ex.R’ failed
The error most likely occurred in:

> ### Name: graticule_labels
> ### Title: Create graticule labels.
> ### Aliases: graticule_labels
> 
> ### ** Examples
> 
> xx <- c(100, 120, 160, 180)
> yy <- c(-80,-70,-60, -50,-45, -30)
> prj <- "+proj=lcc +lon_0=150 +lat_0=-80 +lat_1=-85 +lat_2=-75 +ellps=WGS84"
> plot(graticule(lons = xx, lats = yy,  proj = prj))
Error in sp::spTransform(l, sp::CRS(proj)) : 
  package rgdal is required for spTransform methods
Calls: plot -> graticule -> <Anonymous> -> <Anonymous>
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 38-75 (graticule.Rmd) 
Error: processing vignette 'graticule.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Package unavailable to check Rd xrefs: ‘gRain’
Packages required but not available:
  ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
  ‘EnsDb.Mmusculus.v79’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Package suggested but not available for checking: ‘egg’
Running ‘testpage.R’ [1s/1s]
Running the tests in ‘tests/testpage.R’ failed.
Last 13 lines of output:
  > 
  > 
  > #######################################
  > # Now import testpage.ps and draw it in various ways
  > #######################################
  > 
  > require(grImport)
  Loading required package: grImport
  Loading required package: XML
  > 
  > PostScriptTrace("testpage.ps", "testpage.xml")
  sh: gs: command not found
  Error in PostScriptTrace("testpage.ps", "testpage.xml") : 
    sorry, 'gs' cannot be found
  Execution halted
Errors in running code in vignettes:
when running code in ‘import.Rnw’
  ...

> library("grImport")
Loading required package: XML

> PostScriptTrace("chess_game_01.fromInkscape.eps")
sh: gs: command not found

  When sourcing 'import.R':
Error: sorry, 'gs' cannot be found
Execution halted
when running code in ‘importText.Rnw’
  ...

> library(grImport)
Loading required package: XML

> PostScriptTrace("hello.ps", "hello.xml")
sh: gs: command not found

  When sourcing 'importText.R':
Error: sorry, 'gs' cannot be found
Execution halted
Error in re-building vignettes:
  ...
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

sh: gs: command not found

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in PostScriptTrace("chess_game_01.fromInkscape.eps") : 
  sorry, 'gs' cannot be found
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
cv.plot: no visible global function definition for ‘plot’
cv.plot: no visible global function definition for ‘lines’
cv.plot: no visible global function definition for ‘legend’
path.plot: no visible global function definition for ‘par’
path.plot: no visible global function definition for ‘plot’
path.plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  legend lines par plot
Consider adding
  importFrom("graphics", "legend", "lines", "par", "plot")
to your NAMESPACE file.
Package suggested but not available for checking: ‘impute’
Package required but not available: ‘illuminaio’

Package suggested but not available for checking: ‘brassicaData’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘interval’
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ashg2012.tex' failed.
LaTeX errors:
! LaTeX Error: File `a0poster.cls' not found.

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

! Emergency stop.
<read *> 
         
l.2 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gumbel.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.45 \setmarginsrb
                  {2.9cm}{1.5cm}{2.9cm}{1cm}{\headheight}{\headsep}{\foothei...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgdal’ ‘rgeos’
installed size is 136.1Mb
  sub-directories of 1Mb or more:
    java  134.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/h5.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 67-70 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
HTTP error 403.
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: iterators
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: algorithm did not converge
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Warning: glm.fit: fitted probabilities numerically 0 or 1 occurred
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [67s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(heatwaveR)
  Loading required package: data.table
  Loading required package: ggplot2
  > 
  > test_check("heatwaveR")
  ── 1. Failure: robust = TRUE switches to the slower function (@test-ts2clm.R#59)
  t_2[1] is not strictly less than t_1[1]. Difference: 0.191
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 115 SKIPPED: 0 FAILED: 1
  1. Failure: robust = TRUE switches to the slower function (@test-ts2clm.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘synbreed’
print.tsum: warning in print.default(x$resid, digits = digits, na = "",
  print.gap = 2): partial argument match of 'na' to 'na.print'
print.tsum: no visible global function definition for ‘quantile’
print.tsum: no visible global function definition for ‘printCoefmat’
print.tsum: no visible global function definition for ‘symnum’
tlm: no visible global function definition for ‘formula’
tlm: no visible binding for global variable ‘na.fail’
tlm: no visible global function definition for ‘model.matrix’
tlm: no visible global function definition for ‘model.extract’
tlm: no visible binding for global variable ‘response’
tlm: no visible global function definition for ‘lm.fit’
tlm: no visible global function definition for ‘coef’
tlm: no visible global function definition for ‘resid’
tlm: no visible global function definition for ‘Gamma’
tlm: no visible binding for global variable ‘dofse’
tlm: no visible binding for global variable ‘logLik’
tscore: no visible global function definition for ‘model.extract’
tscore: no visible binding for global variable ‘response’
tscore : <anonymous>: no visible global function definition for
  ‘model.matrix’
tscore: no visible global function definition for ‘resid’
tscore: no visible global function definition for ‘pchisq’
tscore: no visible global function definition for ‘printCoefmat’
tsum: no visible global function definition for ‘pnorm’
tsum: no visible global function definition for ‘pt’
tsum: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  Gamma coef dofse formula lm.fit logLik model.extract model.matrix
  na.fail pchisq pnorm printCoefmat pt quantile resid residuals
  response symnum
Consider adding
  importFrom("stats", "Gamma", "coef", "formula", "lm.fit", "logLik",
             "model.extract", "model.matrix", "na.fail", "pchisq",
             "pnorm", "printCoefmat", "pt", "quantile", "resid",
             "residuals", "symnum")
to your NAMESPACE file.
Package suggested but not available for checking: ‘marray’
Package suggested but not available for checking: ‘RcmdrPlugin.HH’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HiCseg.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
build.clusters.spatial: no visible global function definition for
  ‘kmeans’
build.clusters.spatial: no visible global function definition for
  ‘points’
mubz.copula: no visible global function definition for ‘integrate’
perspcolor: no visible global function definition for ‘terrain.colors’
rCMS: no visible global function definition for ‘runif’
rSchlatherExcess: no visible global function definition for ‘runif’
simul.maxlik.maxstable: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  integrate kmeans points runif terrain.colors
Consider adding
  importFrom("grDevices", "terrain.colors")
  importFrom("graphics", "points")
  importFrom("stats", "integrate", "kmeans", "runif")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/HierO.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        5.4Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/HiPLARM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/HiResTEC.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘qvalue’ ‘pi0’
Package unavailable to check Rd xrefs: ‘pi0’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   4.4Mb
Package suggested but not available for checking: ‘trackr’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HiveR.tex' failed.
LaTeX errors:
! LaTeX Error: File `tufte-handout.cls' not found.

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

! Emergency stop.
<read *> 
         
l.9 \documentclass{tufte-handout}\usepackage
                                            []{graphicx}\usepackage[]{color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (case,noncase) to (1,0)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Class labels have been switched from (No,Yes) to (0,1)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hmeasure.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mice
Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  52 observations with no observed data.  These observations were removed

Warning in hot.deck(isq99, sdCutoff = 3, IDvars = c("IDORIGIN", "YEAR")) :
  45 of 4661 imputations with # donors < 5, consider increasing sdCutoff or using method='p.draw'

* miceadds 2.3-0 (2017-02-21 15:02:53)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Using_Hot_Deck_Data.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {graphicx, subfigure, float} % graphics commands^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

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

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: HSAUR
Loading required package: tools
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch_analysing_longitudinal_dataI.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘hSDM/libs/hSDM.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘useful.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘hSDM.Nmixture.o’, ‘hSDM.Nmixture.iCAR.o’, ‘hSDM.ZIB.o’,
      ‘hSDM.ZIB.iCAR.alteration.o’, ‘hSDM.ZIB.iCAR.o’, ‘hSDM.ZIP.o’,
      ‘hSDM.ZIP.iCAR.alteration.o’, ‘hSDM.ZIP.iCAR.o’,
      ‘hSDM.binomial.o’, ‘hSDM.binomial.iCAR.o’, ‘hSDM.poisson.o’,
      ‘hSDM.poisson.iCAR.o’, ‘hSDM.siteocc.o’, ‘hSDM.siteocc.iCAR.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.18 \usepackage
                [ansinew]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicRanges’ ‘GenomicFeatures’ ‘GenomeInfoDb’ ‘rtracklayer’
  ‘biomaRt’ ‘genoset’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hwde.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \newcommand
               {\keywords}[1]{\addvspace{\baselineskip}\noindent{{\bf Keywor...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'HWEBayes-Guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \renewcommand
                 {\baselinestretch}{1}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘SWAT2R’
'library' or 'require' calls in package code:
  ‘hydroGOF’ ‘hydroTSM’ ‘parallel’ ‘vioplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'hyper2.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

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

Attaching package: ‘Brobdingnag’

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

    max, min, prod, range, sum

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

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

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

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

    sd, sigma

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

    is.primitive

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
start: 300 support points
Iteration 1: 153 support points
Iteration 2: 93 support points
Iteration 3: 54 support points
Iteration 4: 38 support points
Iteration 5: 32 support points
Iteration 6: 29 support points
Iteration 7: 29 support points
spectrum      1:    29 support points, noise = 15.0,   7 iterations
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'baseline.tex' failed.
LaTeX errors:
! LaTeX Error: File `fourier.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                []{helvet}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(IalsaSynthesis)
  > 
  > test_check("IalsaSynthesis")
  Error in loadNamespace(name) : there is no package called 'devtools'
  Calls: test_check ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.1Mb
'library' or 'require' calls to packages already attached by Depends:
  ‘fastICA’ ‘mgcv’
  Please remove these calls from your code.
'library' or 'require' call to ‘wavethresh’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `apa6.cls' not found.

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

! Emergency stop.
<read *> 
         
l.2 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [6s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  testthat results ================================================================
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
Note: found 14 marked Latin-1 strings
  Note: found 39 marked UTF-8 strings
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    data   1.4Mb
    doc    5.1Mb
    libs  10.6Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.6Mb
installed size is 40.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  35.7Mb
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.6Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pritikin-schmidt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  12.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ilc.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     16.3Mb
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/tmp/RtmpPxBOW3/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running ‘testthat.R’ [5s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                AminusB               CminusD AminusB.minus.CminusD 
             0.04765402           -0.04765402            0.09530804 
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.03198493            0.03198493            0.12793972 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#26) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rgeos’
Error in re-building vignettes:
  ...
Loading required package: permute
Warning in wilcox.test.default(indvar.barcelona$B, indvar.moia$B) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(Spec.ind.barcelona, Spec.ind.moia) :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(O.barcelona.ind, O.moia.ind) :
  cannot compute exact p-value with ties
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PigeonExample.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1:   400 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmprMrO6H/x1318db19ee4c/iofile -n -s 2> /dev/null
Warning: running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/x13binary/bin/x13ashtml /tmp/RtmprMrO6H/x1318db19ee4c/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/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/3.4/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  0x1245ac579
#1  0x1245ab945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Error in re-building vignettes:
  ...
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: survival

Attaching package: 'InformativeCensoring'

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

    cox.zph

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'gamma_imputation_Jackson_2014.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.57 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Jeffreys: no visible global function definition for ‘integrate’
Jeffreys: no visible global function definition for ‘splinefun’
count.rows: no visible global function definition for ‘tail’
count.rows: no visible global function definition for ‘head’
cprobs : <anonymous>: no visible global function definition for
  ‘plogis’
inf.func.ltm : f: no visible global function definition for ‘plogis’
infoGPCM: no visible binding for global variable ‘tail’
iota: no visible global function definition for ‘integrate’
iota: no visible global function definition for ‘optimize’
iota: no visible global function definition for ‘pchisq’
iota.c : rirm: no visible global function definition for ‘coef’
iota.c: no visible global function definition for ‘integrate’
iota.c: no visible global function definition for ‘sd’
iota.u: no visible global function definition for ‘integrate’
iprobs : <anonymous>: no visible global function definition for
  ‘plogis’
logL.ltm : logL: no visible global function definition for ‘dbinom’
logL.ltm : logL: no visible global function definition for ‘plogis’
logL.ltm : logL : <anonymous>: no visible global function definition
  for ‘plogis’
probs: no visible global function definition for ‘plogis’
rJeffreys : Jpinv.min: no visible global function definition for
  ‘integrate’
rJeffreys : Jpinv: no visible global function definition for ‘nlminb’
rJeffreys : Jpinv: no visible global function definition for ‘qnorm’
rJeffreys: no visible global function definition for ‘runif’
Undefined global functions or variables:
  coef dbinom head integrate nlminb optimize pchisq plogis qnorm runif
  sd splinefun tail
Consider adding
  importFrom("stats", "coef", "dbinom", "integrate", "nlminb",
             "optimize", "pchisq", "plogis", "qnorm", "runif", "sd",
             "splinefun")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘easypackages’ ‘pacman’
Packages unavailable to check Rd xrefs: ‘easypackages’, ‘pacman’
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking:
  ‘MLP’ ‘org.Hs.eg.db’ ‘a4Base’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Interatrix.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.9Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: MASS
Loading required package: nlme
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'IPMpack_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.7Mb
'library' or 'require' call to ‘HH’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package unavailable to check Rd xrefs: ‘HH’
Errors in running code in vignettes:
when running code in ‘IPSUR.Rnw’
  ...
> library(TeachingDemos)

> plot(z.test(PlantGrowth$weight, stdev = 0.7), "Conf")
Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

  When sourcing 'IPSUR.R':
Error: could not find function "normal.and.t.dist"
Execution halted
Error in re-building vignettes:
  ...

    mnorm

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

    cm

Warning in sqrt(sigma2) : NaNs produced
Warning in sqrt(sigma2) : NaNs produced

Attaching package: 'TeachingDemos'

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

    faces, slider

Loading required package: HH
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'HH'

Error: processing vignette 'IPSUR.Rnw' failed with diagnostics:
 chunk 250 
Error in normal.and.t.dist(mu.H0 = mu, obs.mean = obs.mean, std.dev = std.dev,  : 
  could not find function "normal.and.t.dist"
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘gridExtra’ ‘rBayesianOptimization’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'irace-package.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
.beta.i: no visible global function definition for ‘pnorm’
.chi2.int.test: no visible global function definition for ‘qnorm’
.chi2.int.test: no visible global function definition for ‘pnorm’
.chi2.int.test: no visible global function definition for ‘chisq.test’
.f.int : I: no visible global function definition for ‘pnorm’
.f.int: no visible global function definition for ‘integrate’
.fmod.int : I: no visible global function definition for ‘pnorm’
.fmod.int: no visible global function definition for ‘integrate’
.intervalICC.est1: no visible global function definition for
  ‘constrOptim’
.intervalICC.est2: no visible global function definition for
  ‘constrOptim’
.intervalICC.est3: no visible global function definition for
  ‘constrOptim’
.intervalICC.est4: no visible global function definition for
  ‘constrOptim’
.sigma.int : I: no visible global function definition for ‘pnorm’
.sigma.int : I: no visible global function definition for ‘dnorm’
.sigma.int: no visible global function definition for ‘integrate’
.sigmab.int : I: no visible global function definition for ‘dnorm’
.sigmab.int: no visible global function definition for ‘integrate’
intervalICC.default: no visible global function definition for
  ‘na.omit’
intervalICC.default: no visible global function definition for ‘sd’
intervalICC.default: no visible binding for global variable ‘sd’
ntest.means.default: no visible global function definition for
  ‘na.omit’
ntest.res.default: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  chisq.test constrOptim dnorm integrate na.omit pnorm qnorm sd
Consider adding
  importFrom("stats", "chisq.test", "constrOptim", "dnorm", "integrate",
             "na.omit", "pnorm", "qnorm", "sd")
to your NAMESPACE file.
Package suggested but not available for checking: ‘PMA’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10  \usepackage
                 [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isotone.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘test.R’ [1s/1s]
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > setwd(tempdir())
  > 
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.8Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'JOUS.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {algorithmicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.2Mb
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: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'json-opencpu.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.62 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kcirt.tex' failed.
LaTeX errors:
! LaTeX Error: File `supertabular.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
Error in re-building vignettes:
  ...
Loading required package: ade4
Loading required package: lattice
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'simulation.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \title
          {KDETrees Simulations}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   7.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titling.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘stsm’
Package unavailable to check Rd xrefs: ‘stsm’
Running examples in ‘KFKSDS-Ex.R’ failed
The error most likely occurred in:

> ### Name: DS
> ### Title: Disturbance Smoother for State Space Models
> ### Aliases: DS DS.deriv
> ### Keywords: ts, model
> 
> ### ** Examples
> 
> # local level plus seasonal model with arbitrary parameter values
> # for the 'JohnsonJohnson' time series
> m <- stsm::stsm.model(model = "llm+seas", y = JohnsonJohnson, 
+   pars = c("var1" = 2, "var2" = 15, "var3" = 30))
Error in loadNamespace(name) : there is no package called ‘stsm’
Calls: :: ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \input
          {header}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘illustration.png’, ‘kinn.Rmd’
Package has no Sweave vignette sources and no VignetteBuilder field.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/kmcudaR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: knotR
Warning in plot.window(...) : "box" is not a graphical parameter
Warning in plot.xy(xy, type, ...) : "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in axis(side = side, at = at, labels = labels, ...) :
  "box" is not a graphical parameter
Warning in box(...) : "box" is not a graphical parameter
Warning in title(...) : "box" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'knot.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

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

Warning: Removed 27 rows containing missing values (geom_path).
Scale for 'y' is already present. Adding another scale for 'y', which will
replace the existing scale.
Scale for 'x' is already present. Adding another scale for 'x', which will
replace the existing scale.
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 8 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kobe.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.24 \usepackage
                {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'koRpus_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.8Mb
Running examples in ‘kstIO-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_kbase
> ### Title: Read base file
> ### Aliases: read_kbase
> ### Keywords: file
> 
> ### ** Examples
> 
> # Produce a base file
> library(kst)
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
> data(DoignonFalmagne7)
> b <- kbase(kspace(kstructure(as.pattern(DoignonFalmagne7$K, as.set=TRUE))))
> write_kbase(b, "DF7.bas", "KST") # (Old) KST format
Error in write_kbase(b, "DF7.bas", "KST") : 
  “x” must be of class “kbase” or “matrix”!
Execution halted
Errors in running code in vignettes:
when running code in ‘kstIO.Rnw’
  ...

> write_kstructure(ksp, "DF7.struct")

> write_kspace(ksp, "DF7.space", format = "matrix")

> write_kbase(b, "DF7.bas", format = "KST")

  When sourcing ‘kstIO.R’:
Error: “x” must be of class “kbase” or “matrix”!
Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘stringr’

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

    %>%

Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 2 (label = write-functions) 
Error in write_kbase(b, "DF7.bas", format = "KST") : 
  “x” must be of class “kbase” or “matrix”!
Execution halted
Package required and available but unsuitable version: ‘relations’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Unexported object imported by a ':::' call: ‘stats:::plotNode’
  See the note in ?`:::` about the use of this operator.
colorplot : dendroploth: no visible global function definition for
  ‘plot’
colorplot : dendroploth: no visible global function definition for
  ‘par’
colorplot : dendroploth: no visible global function definition for
  ‘rainbow’
colorplot : dendroploth: no visible global function definition for
  ‘abline’
colorplot : dendroplotv: no visible global function definition for
  ‘plot’
colorplot : dendroplotv: no visible global function definition for
  ‘par’
colorplot : dendroplotv: no visible global function definition for
  ‘rainbow’
colorplot : dendroplotv: no visible global function definition for
  ‘abline’
colorplot: no visible global function definition for ‘as.dendrogram’
plot.labclust: no visible global function definition for ‘plot’
plot.labclust: no visible global function definition for
  ‘as.dendrogram’
Undefined global functions or variables:
  abline as.dendrogram par plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "par", "plot")
  importFrom("stats", "as.dendrogram")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: boot
Loading required package: MASS
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'laeken-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `soul.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘R2jags’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/LANDD.Rcheck/00install.out’ for details.
installed size is 79.3Mb
  sub-directories of 1Mb or more:
    libs  78.0Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    libs          11.5Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    dataset   1.4Mb
    include  11.8Mb
    libs      3.4Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.19 \usepackage
                {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘topicmodels’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'details.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.60 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘rjags’
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LFDREmpiricalBayes.tex' failed.
LaTeX errors:
! LaTeX Error: File `changepage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/libstableR.Rcheck/00install.out’ for details.
LinearizedSVRTrain: no visible global function definition for ‘kmeans’
sigma.est: no visible global function definition for ‘median’
sigma.est: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist kmeans median
Consider adding
  importFrom("stats", "dist", "kmeans", "median")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
For a step-by-step guide to using linkcomm functions:
   > vignette(topic = "linkcomm", package = "linkcomm")
To run an interactive demo:
   > demo(topic = "linkcomm", package = "linkcomm")
To cite, see:
   > citation("linkcomm")
NOTE: To use linkcomm, you require read and write permissions in the current directory (see: help("getwd"), help("setwd"))

The "ward" method has been renamed to "ward.D"; note new "ward.D2"
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'linkcomm.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'LinRegInteractive.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {booktabs}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.8Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs      21.0Mb
    testdata   1.6Mb
Package required but not available: ‘LDheatmap’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmm-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Calls with DUP:
   .C("d2Dsigma", x1 = as.double(x[, 1]), x2 = as.double(x[, 2]), 
       y1 = as.double(y[, 1]), y2 = as.double(y[, 2]), sigma = as.double(sigma), 
       nx = as.integer(nx), ny = as.integer(ny), depth = as.double(depth), 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "localdepth")
   .C("ldcircsimp", x = as.double(x), y = as.double(y), nx = as.integer(nx), 
       ny = as.integer(ny), tau = as.double(tau), nuse = as.integer(nuse), 
       depth = as.double(depth), localdepth = as.double(localdepth), 
       diameters = as.double(diameters), DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "localdepth")
   .C("ld2Ddiamsimp", x1 = as.double(x[, 1]), x2 = as.double(x[, 
       2]), y1 = as.double(y[, 1]), y2 = as.double(y[, 2]), tau = as.double(tau), 
       nx = as.integer(nx), ny = as.integer(ny), depth = as.double(depth), 
       localdepth = as.double(localdepth), DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "localdepth")
   .C("ld2Dareasimp", x1 = as.double(x[, 1]), x2 = as.double(x[, 
       2]), y1 = as.double(y[, 1]), y2 = as.double(y[, 2]), tau = as.double(tau), 
       nx = as.integer(nx), ny = as.integer(ny), depth = as.double(depth), 
       localdepth = as.double(localdepth), DUP = FALSE, NAOK = FALSE, 
       PACKAGE = "localdepth")
   .C("twoDdiam", x = as.double(x[, 1]), y = as.double(x[, 2]), 
       nx = as.integer(nx), result = as.double(result), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "localdepth")
   .C("twoDarea", x = as.double(x[, 1]), y = as.double(x[, 2]), 
       nx = as.integer(nx), result = as.double(result), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "localdepth")
   .C("oneDdiam", x = as.double(x), nx = as.integer(nx), result = as.double(result), 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "localdepth")
   .C("circdiam", x = as.double(x), nx = as.integer(nx), diameters = as.double(diameters), 
       DUP = FALSE, NAOK = FALSE, PACKAGE = "localdepth")
DUP is no longer supported and will be ignored.
hsnorm: no visible global function definition for ‘qnorm’
hsnorm: no visible global function definition for ‘pnorm’
localdepth.mahalanobis: no visible global function definition for ‘cov’
localdepth.similarity.mahalanobis: no visible global function
  definition for ‘cov’
localdepth.simp.approx.internal: no visible global function definition
  for ‘cov’
lsdnorm: no visible global function definition for ‘qnorm’
lsdnorm : ldnorm.int : pdf: no visible global function definition for
  ‘dnorm’
lsdnorm : ldnorm.int : cdf: no visible global function definition for
  ‘pnorm’
lsdnorm : ldnorm.int : integr1: no visible global function definition
  for ‘integrate’
lsdnorm : ldnorm.int : integr2: no visible global function definition
  for ‘integrate’
plot.localdepth: no visible global function definition for ‘plot’
plot.localdepth: no visible global function definition for ‘text’
quantile.mahalanobis: no visible global function definition for ‘cov’
sdnorm: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cov dnorm integrate plot pnorm qnorm text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cov", "dnorm", "integrate", "pnorm", "qnorm")
to your NAMESPACE file.
Running examples in ‘localsolver-Ex.R’ failed
The error most likely occurred in:

> ### Name: add.output.expr
> ### Title: Add expression to output of ls.problem.
> ### Aliases: add.output.expr
> 
> ### ** Examples
> 
> model.text.lsp <- lsp.model.example('extdata/knapsack.txt')
> lsp <- ls.problem(model.text.lsp)
sh: localsolver: command not found
Error: has.localsolver(ls.path) is not TRUE
Execution halted
lines_LCObject: no visible global function definition for ‘lines’
lines_LCPHObject: no visible global function definition for ‘lines’
plot_LCObject: no visible global function definition for ‘plot’
plot_LCPHObject: no visible global function definition for ‘plot’
qLC: no visible global function definition for ‘optimize’
simPH_Censored: no visible global function definition for ‘runif’
simPH_Censored: no visible global function definition for ‘rnorm’
simPH_Censored: no visible global function definition for ‘rgamma’
sim_Censored: no visible global function definition for ‘rbeta’
sim_Censored: no visible global function definition for ‘runif’
start.Inf: no visible global function definition for ‘sd’
Undefined global functions or variables:
  lines optimize plot rbeta rgamma rnorm runif sd
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "optimize", "rbeta", "rgamma", "rnorm", "runif",
             "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plotGlm.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Call with DUP:
   .Fortran(lpepa_s, x, y, as.integer(n), bandwidth = bandwidth, 
       deriv = as.integer(deriv), order = as.integer(order), x.out = x.out, 
       as.integer(n.out), as.integer(mnew), integer(nmoms), double(nmoms * 
           4 * (2 + order + as.integer(var))), est = double(n.out), 
       as.integer(leng), nmoms, var = as.integer(var), est.var = double(n.out), 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 15-33 (README.Rmd) 
Error: processing vignette 'README.Rmd' failed with diagnostics:
object 'params' not found
Execution halted
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  43.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: lucid
Loading required package: lattice
Loading required package: rjags
Quitting from lines 269-293 (lucid_printing.Rmd) 
Error: processing vignette 'lucid_printing.Rmd' failed with diagnostics:
could not find function "jags.model"
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.5Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data  16.0Mb
Delta_c: no visible global function definition for ‘pnorm’
Gamma_c: no visible global function definition for ‘dnorm’
Psi_c: no visible global function definition for ‘pnorm’
Rho_c: no visible global function definition for ‘pnorm’
Theta_c: no visible global function definition for ‘pnorm’
Theta_c: no visible global function definition for ‘dnorm’
Vega_c: no visible global function definition for ‘dnorm’
blackScholes: no visible global function definition for ‘pnorm’
currentStocks: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  dnorm pnorm read.csv
Consider adding
  importFrom("stats", "dnorm", "pnorm")
  importFrom("utils", "read.csv")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bdt.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                [margin=1.0in]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.4Mb
  sub-directories of 1Mb or more:
    libs  24.1Mb
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.4Mb
Error in re-building vignettes:
  ...
Loading required package: magree
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'landis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GO.db’ ‘RGtk2’ ‘gWidgetsRGtk2’ ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
Error in re-building vignettes:
  ...
Loading required package: Matrix
Loading required package: quadprog
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Mangrove.tex' failed.
LaTeX errors:
! LaTeX Error: File `moreverb.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
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]="./webshot875a24484c01.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot875a24484c01.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning 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]="./webshot160865158fff6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot160865158fff6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Missing or unexported object: ‘spatstat::is.hole.xypolygon’
Error in re-building vignettes:
  ...
Loading required package: sp
Checking rgeos availability: TRUE
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: use rgdal::readOGR or sf::st_read
Warning: non-unique values when setting 'row.names': ‘37055’, ‘37095’

Error: processing vignette 'combine_maptools.Rnw' failed with diagnostics:
 chunk 18 
Error in unionSpatialPolygons(nc90, IDs = paste(nc90$ST, nc90$CO, sep = "")) : 
  package rgeos required for unionSpatialPolygons
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.1Mb
Package required and available but unsuitable version: ‘rcbsubset’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
Error in re-building vignettes:
  ...

Loading required package: sandwich

Attaching package: ‘party’

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

    varimp

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

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

! Emergency stop.
<read *> 
         
l.31 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CourseNotes.tex' failed.
LaTeX errors:
! LaTeX Error: File `tocbibind.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {makeidx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    libs  23.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mcmcse_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.78 \title
           {An Introduction to Estimating Monte Carlo Standard Errors with R...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mdendro.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   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.
Quitting from lines 228-229 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.4Mb
Error in re-building vignettes:
  ...
Loading required package: meteoland
Loading required package: sp
Loading required package: qmap
Loading required package: fitdistrplus
Loading required package: MASS
Loading required package: survival
Loading required package: spdep
Loading required package: Matrix
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'FireBehaviour.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

Effect decomposition on the scale of the linear predictor
conditional on: gender, educ, age 
with x* = 0, x = 1

Effect decomposition on exp(scale of the linear predictor)
conditional on: gender, educ, age 
with x* = 0, x = 1

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

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mediation-old.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.47 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘medSTC/libs/medSTC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘medstc/medstc.o’, ‘medstc/corpus.o’,
      ‘svmlight/svm_common.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘medstc/corpus.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package unavailable to check Rd xrefs: ‘untb’
Packages suggested but not available for checking:
  ‘TxDb.Hsapiens.UCSC.hg19.knownGene’ ‘org.Hs.eg.db’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'memgeneTutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \usepackage
                {parskip}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘aws.s3’
Package suggested but not available for checking: ‘rstanarm’
Error in re-building vignettes:
  ...

arm (Version 1.9-3, built: 2016-11-21)

Working directory is /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/merTools.Rcheck/vign_test/merTools/vignettes

Loading required package: dplyr

Attaching package: 'dplyr'

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

    select

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 320-333 (Using_predictInterval.Rmd) 
Error: processing vignette 'Using_predictInterval.Rmd' failed with diagnostics:
there is no package called 'rstanarm'
Execution halted
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.4Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.4Mb
Package required and available but unsuitable version: ‘sybil’

Packages suggested but not available for checking: ‘clpAPI’ ‘glpkAPI’ ‘ctc’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘GEOquery’ ‘org.Hs.eg.db’ ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’
  ‘hgu95av2.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'metaMA.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GEOquery’ ‘affy’ ‘hgu133plus2.db’ ‘doSMP’ ‘impute’
Packages suggested but not available for checking:
  ‘HTSFilter’ ‘DESeq’ ‘DESeq2’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’
Execution halted
Running examples in ‘metaSEM-Ex.R’ failed
The error most likely occurred in:

> ### Name: indirectEffect
> ### Title: Estimate the asymptotic covariance matrix of standardized or
> ###   unstandardized indirect and direct effects
> ### Aliases: indirectEffect
> ### Keywords: compute effect sizes
> 
> ### ** Examples
> 
> ## A correlation matrix as input
> x <- matrix(c(1, 0.4, 0.2, 0.4, 1, 0.3, 0.2, 0.3, 1), ncol=3)
> dimnames(x) <- list( c("y", "m", "x"), c("y", "m", "x") )
> indirectEffect(x, n=300)
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: indirectEffect -> mxRun -> runHelper
Execution halted
Packages suggested but not available for checking: ‘BRugs’ ‘rjags’
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  12.6Mb
    misc   1.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhde_article.tex' failed.
LaTeX errors:
! LaTeX Error: File `tabulary.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette1.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \IfFileExists
                  {upquote.sty}{\usepackage{upquote}}{}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: survival
Loading required package: texreg
Version:  1.36.23
Date:     2017-03-03
Author:   Philip Leifeld (University of Glasgow)

Please cite the JSS article in your publications -- see citation("texreg").
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mhurdle.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {amssymb, amsfonts}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
File ‘MigClim/libs/MigClim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’, ‘src_cell.o’, ‘validate.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Objects: ‘genclust.o’, ‘migrate.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `blindtext.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [bf]{caption2}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mixor.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [19s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(mizer)
  > 
  > test_check("mizer")
  ── 1. Failure: retune_abundance reproduces scaling model (@test-wrapper_function
  max(abs(initial_n - pr@initial_n)) is not strictly less than 2e-11. Difference: 1.09e-11
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 508 SKIPPED: 1 FAILED: 1
  1. Failure: retune_abundance reproduces scaling model (@test-wrapper_functions.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Package unavailable to check Rd xrefs: ‘genefilter’
installed size is 42.2Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.7Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.136 0.007 0.145
Execution halted
Error in re-building vignettes:
  ...
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in split.default(x = seq_len(nrow(x)), f = f, drop = drop, ...) :
  data length is not a multiple of split variable
Warning in lmList(normexam ~ standLRT + sex | school, Exam, subset = type ==  :
  Fitting failed for 1 group(s), probably because a factor only had one level
refitting model(s) with ML (instead of REML)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'StarData.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
VarCor: no visible binding for global variable ‘var’
VarCor: no visible global function definition for ‘var’
VarCor: no visible global function definition for ‘cor’
lmcv: no visible global function definition for ‘lm’
lmcv: no visible global function definition for ‘predict’
plotcor: no visible global function definition for ‘cor’
plotcor: no visible global function definition for ‘par’
plotcor: no visible global function definition for ‘hist’
plotcor: no visible global function definition for ‘axis’
plotcor: no visible global function definition for ‘text’
plotcor: no visible global function definition for ‘box’
plotvar: no visible global function definition for ‘par’
plotvar: no visible binding for global variable ‘var’
plotvar: no visible global function definition for ‘var’
plotvar: no visible global function definition for ‘hist’
plotvar: no visible global function definition for ‘text’
plotvar: no visible global function definition for ‘box’
plotvar: no visible global function definition for ‘points’
stepMLRMPA: no visible global function definition for ‘write.table’
stepMLRMPA: no visible global function definition for ‘lm’
stepMLRMPA: no visible global function definition for ‘step’
stepMLRMPA: no visible global function definition for ‘predict’
Undefined global functions or variables:
  axis box cor hist lm par points predict step text var write.table
Consider adding
  importFrom("graphics", "axis", "box", "hist", "par", "points", "text")
  importFrom("stats", "cor", "lm", "predict", "step", "var")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Running ‘run-base.R’ [410s/313s]
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2964 SKIPPED: 1 FAILED: 14
  1. Error: plotFilterValues (@test_base_generateFilterValuesData.R#73) 
  2. Error: args are passed down to filter methods (@test_base_generateFilterValuesData.R#97) 
  3. Error: 2 hyperparams (@test_base_generateHyperParsEffect.R#174) 
  4. Error: 2 hyperparams nested (@test_base_generateHyperParsEffect.R#230) 
  5. Error: getHyperPars (@test_base_getHyperPars.R#19) 
  6. Error: WeightedClassesWrapper, binary (@test_base_imbal_weightedclasses.R#16) 
  7. Error: WeightedClassesWrapper, multiclass (@test_base_imbal_weightedclasses.R#41) 
  8. Error: getClassWeightParam (@test_base_imbal_weightedclasses.R#72) 
  9. Error: measures (@test_base_measures.R#53) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 32.0Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mmap.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \hypersetup
               {colorlinks,%^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
contrandz: no visible global function definition for ‘runif’
dfupdatefun: no visible global function definition for ‘uniroot’
kmeansz: no visible global function definition for ‘kmeans’
plot.mmtfa: no visible global function definition for ‘rainbow’
plot.mmtfa: no visible global function definition for ‘par’
plot.mmtfa: no visible global function definition for ‘plot’
plot.mmtfa: no visible global function definition for ‘title’
plot.mmtfa: no visible global function definition for ‘contour’
plot.mmtfa: no visible global function definition for ‘rgb’
plot.mmtfa : dunivt: no visible global function definition for
  ‘mahalanobis’
plot.mmtfa : dunivt: no visible global function definition for ‘dnorm’
plot.mmtfa: no visible global function definition for ‘density’
plot.mmtfa: no visible global function definition for ‘curve’
sginit: no visible global function definition for ‘cov.wt’
sgupdate: no visible global function definition for ‘cov.wt’
winit: no visible global function definition for ‘mahalanobis’
Undefined global functions or variables:
  contour cov.wt curve density dnorm kmeans mahalanobis par plot
  rainbow rgb runif title uniroot
Consider adding
  importFrom("grDevices", "rainbow", "rgb")
  importFrom("graphics", "contour", "curve", "par", "plot", "title")
  importFrom("stats", "cov.wt", "density", "dnorm", "kmeans",
             "mahalanobis", "runif", "uniroot")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MNP.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.29 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘cclust’ ‘clv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
clusval: no visible global function definition for ‘std.ext’
clusval: no visible global function definition for ‘confusion.matrix’
clusval: no visible global function definition for ‘similarity.index’
clusval: no visible global function definition for ‘clv.Jaccard’
clusval: no visible global function definition for ‘clv.Folkes.Mallows’
cross.quant.similarity: no visible global function definition for
  ‘dist’
getParetoRanking: no visible global function definition for ‘na.omit’
getParetoSet: no visible global function definition for ‘na.omit’
mocca.validate: no visible global function definition for ‘combn’
plot.mocca.objectives: no visible global function definition for ‘plot’
plot.mocca.objectives: no visible global function definition for ‘text’
predict_baseline: no visible global function definition for ‘knn1’
predict_cclust: no visible global function definition for ‘cclust’
predict_cclust: no visible global function definition for ‘predict’
predict_kmeans: no visible global function definition for ‘kmeans’
predict_kmeans: no visible global function definition for ‘knn1’
predict_single: no visible global function definition for ‘cutree’
predict_single: no visible global function definition for ‘agnes’
predict_single: no visible global function definition for ‘knn1’
Undefined global functions or variables:
  agnes cclust clv.Folkes.Mallows clv.Jaccard combn confusion.matrix
  cutree dist kmeans knn1 na.omit plot predict similarity.index std.ext
  text
Consider adding
  importFrom("graphics", "plot", "text")
  importFrom("stats", "cutree", "dist", "kmeans", "na.omit", "predict")
  importFrom("utils", "combn")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: rgdal
rgdal: version: 1.2-6, (SVN revision 651)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/rgdal/proj
 Linking to sp version: 1.2-4 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ExploreModelMap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \setlength
              {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modelObj.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘Test.R’ [2s/10s]
Running the tests in ‘tests/Test.R’ failed.
Last 13 lines of output:
  +   Dates <- GetDates(SubsetExample$lat, SubsetExample$long, Product)[1:2]
  + 
  +   GetSubset(Lat = SubsetExample$lat, Long = SubsetExample$long, Product = Product, Band = Band,
  +             StartDate = Dates[1], EndDate = Dates[1], KmAboveBelow = 0, KmLeftRight = 0)
  + 
  +   MODISSubsets(LoadDat = SubsetExample, Product = "MCD12Q1", Bands = c("Land_Cover_Type_1"),
  +                Size = c(1,1), StartDate = TRUE)
  + 
  +   MODISSummaries(LoadDat = SubsetExample, Product = "MCD12Q1", Band = "Land_Cover_Type_1",
  +                  ValidRange = c(0,254), NoDataFill = 255, ScaleFactor = 1, StartDate = TRUE)
  + }
  Error in Product == GetProducts() : 
    comparison of these types is not implemented
  Calls: GetBands
  Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingMODISTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-17. For overview type 'help("mgcv-package")'.
Loading required package: splines
Warning: max number of iterations attained
Warning: max number of iterations attained
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.70 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.7Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    libs  12.9Mb
Package unavailable to check Rd xrefs: ‘seewave’
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   4.8Mb
Packages suggested but not available for checking:
  ‘CGHcall’ ‘aroma.affymetrix’ ‘aroma.cn’ ‘aroma.core’ ‘aroma.light’
'library' or 'require' calls in package code:
  ‘R.devices’ ‘R.filesets’ ‘R.methodsS3’ ‘R.oo’ ‘aroma.affymetrix’
  ‘aroma.cn’ ‘aroma.core’ ‘aroma.light’ ‘matrixStats’ ‘snowfall’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Unexported object imported by a ':::' call: ‘cghseg:::segmeanCO’
  See the note in ?`:::` about the use of this operator.
perf.sphere.dim: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rnorm
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
File ‘mph/libs/mph.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mph.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mph.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘asreml’ ‘happy.hbrem’ ‘Heatplus’ ‘VPdtw’
'library' or 'require' calls to packages already attached by Depends:
  ‘gdata’ ‘seriation’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘Heatplus’ ‘VPdtw’ ‘aod’ ‘asreml’ ‘happy.hbrem’ ‘lattice’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘gdata’ ‘seriation’ ‘wgaim’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘qtl:::readMWril’
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  ‘qtl:::adjust.rf.ri’ ‘qtl:::plot.scanone’ ‘qtl:::ripple.perm1’
  ‘qtl:::ripple.perm2’ ‘qtl:::testchr’
  See the note in ?`:::` about the use of this operator.
Foreign function calls to a different package:
  .C("R_reorgRIgenoprob", ..., PACKAGE = "qtl")
  .C(cfunc, ..., PACKAGE = "qtl")
  .C(func, ..., PACKAGE = "qtl")
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘mpMap-Ex.R’ failed
The error most likely occurred in:

> ### Name: findqtl2
> ### Title: Detect a second QTL in a QTL profile from (composite) interval
> ###   mapping
> ### Aliases: findqtl2
> 
> ### ** Examples
> 
> sim.map <- sim.map(len=rep(100, 2), n.mar=11, include.x=FALSE, eq.spacing=TRUE)
> sim.ped <- sim.mpped(4, 1, 500, 6, 1)
> sim.dat <- sim.mpcross(map=sim.map, pedigree=sim.ped, qtl=matrix(data=c(1, 10, .4, 0, 0, 0, 1, 70, 0, .35, 0, 0), nrow=2, ncol=6, byrow=TRUE), seed=1)
> mpp.dat <- mpprob(sim.dat, program="qtl", step=2)
[1] "No chromosomes specified, will default to all"
 --Read the following data:
	 500  individuals
	 20  markers
	 2  phenotypes
> mpq.dat <- mpIM(object=mpp.dat, ncov=0, responsename="pheno")
 --Read the following data:
	 500  individuals
	 20  markers
	 2  phenotypes
Loading required package: aod
------Analyzing Chr  1 ----------
------Analyzing Chr  2 ----------
> mpq2 <- findqtl2(mpq.dat, drop=2)
Loading required package: VPdtw
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘VPdtw’
Error in dilation(cpv2, dwindow) : could not find function "dilation"
Calls: findqtl2
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mptinr_introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `threeparttable.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgdal’ ‘devtools’
Running examples in ‘mptools-Ex.R’ failed
The error most likely occurred in:

> ### Name: mp2sp
> ### Title: Create a SpatialPointsDataFrame describing Metapop population
> ###   centroids
> ### Aliases: mp2sp
> ### Keywords: spatial
> 
> ### ** Examples
> 
> mp <- system.file('example.mp', package='mptools')
> r <- system.file('example_001.tif', package='mptools')
> coords <- mp2xy(mp, r, 9.975)
Error in .rasterObjectFromFile(x, band = band, objecttype = "RasterLayer",  : 
  Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Calls: mp2xy ... <Anonymous> -> <Anonymous> -> .local -> .rasterObjectFromFile
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.
Extracting simulation results from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Extracting population metadata from file:
/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/mptools.Rcheck/mptools/example.mp
Quitting from lines 136-140 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Cannot create RasterLayer object from this file; perhaps you need to install rgdal first
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MRCV-vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.100 \usepackage
                 {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  12.5Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

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

Packages suggested but not available for checking:
  ‘GO.db’ ‘org.Hs.eg.db’ ‘org.Mm.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package unavailable to check Rd xrefs: ‘Biostrings’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/MSeasy.Rcheck/00install.out’ for details.
Package required but not available: ‘MSeasy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 39.4Mb
  sub-directories of 1Mb or more:
    libs  39.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: xgettext: command not found
sh: msgmerge: command not found
sh: msgmerge: command not found
sh: msgfmt: command not found
sh: msgconv: command not found
Quitting from lines 136-138 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
running msgconv on 'R-en@quot' UTF-8 localization failed
Execution halted
Package suggested but not available for checking: ‘pgirmess’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SIRtrans.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.71 \usepackage
                {mathtools}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    libs  57.1Mb
Error in re-building vignettes:
  ...

Attaching package: ‘multivator’

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

    levels, rbind

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘purrrlyr’
  All declared Imports should be used.
Package suggested but not available for checking: ‘BiocInstaller’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

Warning in coxdetails$hazard/exp(apply(coxdetails$x, 2, mean) %*% beta) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in ((C[exposureindex, ] - C[nexposures + 1, ]) %*% covariatesurvs) *  :
  Recycling array of length 1 in array-vector arithmetic is deprecated.
  Use c() or as.vector() instead.

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

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {psfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available: ‘AnnotationDbi’ ‘graph’ ‘samr’

Package suggested but not available for checking: ‘KEGG.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   4.0Mb
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...

trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/Sampson.zip'
Content type 'application/zip' length 2182 bytes
==================================================
downloaded 2182 bytes

Warning in get.vertex.attribute.active(net, "happiness", onset = 2.5, terminus = 4.5) :
  Multiple attribute values matched query spell for attribute happiness.active on some vertices. Only earliest value used

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

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {color}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 31.8Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              3.4Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.4Mb
    tests          1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Running ‘test-all.R’ [26s/27s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  5: getNamespace(ns)
  6: tryCatch(loadNamespace(name), error = function(e) stop(e))
  7: tryCatchList(expr, classes, parentenv, handlers)
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  
  Error in library(devtools) : there is no package called 'devtools'
  Calls: <Anonymous> ... with_reporter -> force -> source_file -> eval -> eval -> library
  testthat results ================================================================
  OK: 198 SKIPPED: 0 FAILED: 2
  1. Error: Nlsy79Gen2 (@test-column-utilities.R#89) 
  2. Error: RenameNlsyColumn (@test-column-utilities.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
plot.isp: no visible global function definition for ‘median’
plot.isp: no visible global function definition for ‘plot’
plot.isp: no visible global function definition for ‘lines’
plot.nmcd: no visible global function definition for ‘median’
plot.nmcd: no visible global function definition for ‘plot’
plot.nmcd: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines median plot
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeSystemARPACK
Apr 03, 2017 6:54:41 AM com.github.fommil.netlib.ARPACK <clinit>
WARNING: Failed to load implementation from: com.github.fommil.netlib.NativeRefARPACK
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'NoiseFiltersR.tex' failed.
LaTeX errors:
! LaTeX Error: File `stmaryrd.sty' not found.

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

! Emergency stop.
<read *> 
         
l.73 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nonrandom.tex' failed.
LaTeX errors:
! LaTeX Error: File `sfmath.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nopaco.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...

 You can now run (pdf)latex on ‘noweb.tex’ 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'noweb.tex' failed.
LaTeX errors:
! LaTeX Error: File `comment.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespace in Imports field not imported from: ‘stats’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘mclust’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'nplr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 \setlength
               {\parskip}{0.7ex plus0.1ex minus0.1ex}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
2: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
3: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
4: In nlm(f = .sce, p = .initPars(x, y, 5), x = x, yobs = y, .weight,  :
  NA/Inf replaced by maximum positive value
Execution halted
Packages required but not available: ‘aroma.core’ ‘aroma.affymetrix’

Depends: includes the non-default packages:
  ‘R.methodsS3’ ‘MASS’ ‘matrixStats’ ‘R.oo’ ‘R.utils’ ‘aroma.core’
  ‘aroma.affymetrix’ ‘DNAcopy’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   7.2Mb
Error in re-building vignettes:
  ...
     
     taxi <- etl("nyctaxi", dir = "~/Desktop/nyctaxi/")
     taxi %>% 
        etl_extract(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_transform(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_load(years = 2016, months = 1:2, types = c("yellow","green")) 
     ## End(Not run)
     


Attaching package: 'lubridate'

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]="./webshotc7e03817d7c8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc7e03817d7c8.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Loading required package: xml2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'oaih.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Unexported object imported by a ':::' call: ‘tree:::tree.matrix’
  See the note in ?`:::` about the use of this operator.
File ‘oblique.tree/libs/oblique.tree.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
Error in re-building vignettes:
  ...
Loading required package: lattice
Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

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

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
odfTable.table: no visible global function definition for ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is 75.2Mb
  sub-directories of 1Mb or more:
    libs  74.8Mb
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Actual value: "c++ exception (unknown reason)"
  
  
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  error$message does not match "The length value".
  Actual value: "c++ exception (unknown reason)"
  
  
  testthat results ================================================================
  OK: 34 SKIPPED: 0 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
Running ‘testthat.R’ [12s/12s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > library(ROI)
  ROI.plugin.scs: R Optimization Infrastructure
  Registered solver plugins: nlminb, alabama, deoptim, ecos, ipop, lpsolve, msbinlp, nloptr, optimx, qpoases, quadprog, scs.
  Default solver: auto.
  > library(ROI.plugin.glpk)
  Error in library(ROI.plugin.glpk) : 
    there is no package called 'ROI.plugin.glpk'
  Execution halted
Error in re-building vignettes:
  ...
dev.new(): using pdf(file="Rplots3.pdf")
dev.new(): using pdf(file="Rplots4.pdf")
dev.new(): using pdf(file="Rplots5.pdf")
dev.new(): using pdf(file="Rplots6.pdf")
dev.new(): using pdf(file="Rplots7.pdf")
dev.new(): using pdf(file="Rplots8.pdf")
dev.new(): using pdf(file="Rplots9.pdf")
dev.new(): using pdf(file="Rplots10.pdf")
dev.new(): using pdf(file="Rplots11.pdf")
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: File `varwidth.sty' not found.

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

! Emergency stop.
<read *> 
         
l.69 \RequirePackage{varwidth}[2009/03/30]
                                          ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  "phi" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "box" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "r" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "theta" is not a graphical parameter
Warning in plot.xy(xy.coords(x, y), type = type, ...) :
  "phi" is not a graphical parameter
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onionpaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: minpack.lm
Waiting for profiling to be done...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'onls.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘ontologyPlot’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 80-92 (intro-to-ontologyX.Rmd) 
Error: processing vignette 'intro-to-ontologyX.Rmd' failed with diagnostics:
there is no package called 'ontologyPlot'
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/OpenCL.Rcheck/00install.out’ for details.
installed size is 113.2Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    103.3Mb
    models    4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$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]="./webshota5057ab2ba73.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshota5057ab2ba73.png': No such file or directory
Quitting from lines 22-24 (openwindfarm-vignette.Rmd) 
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Packages suggested but not available for checking:
  ‘Biobase’ ‘annotate’ ‘GO.db’ ‘org.At.tair.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'optimbase_manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: clinfun
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OptInterim.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.17 \usepackage
                {algorithm2e}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package which this enhances but not available for checking: ‘graph’
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Error in .requirePackage(package) : 
  unable to find required package ‘Biobase’
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  Calls: <Anonymous> ... .extendsForS3 -> extends -> getClassDef -> .requirePackage
  Execution halted
Errors in running code in vignettes:
when running code in ‘ordinalgmifs.Rnw’
  ...
Loading required package: survival

> data(hccframe)

> cumulative.logit <- ordinal.gmifs(group ~ 1, x = hccframe[, 
+     -1], data = hccframe)

Execution halted

... incomplete output.  Crash?
Packages suggested but not available for checking: ‘IsoGene’ ‘Biobase’
Error in re-building vignettes:
  ...
Loading required package: orgutils
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'orgutils_examples.tex' failed.
LaTeX errors:
! LaTeX Error: File `libertine.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [scaled=0.8]{DejaVuSansMono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Peer certificate cannot be authenticated with given CA certificates
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  testthat results ================================================================
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.7Mb
Error in re-building vignettes:
  ...
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: Removed 575 rows containing non-finite values
(stat_density).
Warning: Removed 2 rows containing missing values (geom_vline).
Warning: Removed 370 rows containing missing values (geom_point).
Warning: Removed 370 rows containing missing values (geom_point).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'P2C2M_Vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DEU_PISA2012_description.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               {tabularx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pan-tr.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath,epsfig}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Factors are dropped from the summary
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Factors are dropped from the summary
Non-factors are dropped from the summary
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'papeR_with_latex.tex' failed.
LaTeX errors:
! LaTeX Error: File `capt-of.sty' not found.

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

! Emergency stop.
<read *> 
         
l.55 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘pcalg’ ‘Rgraphviz’
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'parfm.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 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
Warning: Column `party_id` joining character vector and factor, coercing into character vector
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]="./webshotff4c700f680.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotff4c700f680.png': No such file or directory
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partDSAvig.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: partitions
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partitionspaper.tex' failed.
LaTeX errors:
! LaTeX Error: File `dsfont.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {bbm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'partsm.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.47 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘glmnet’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cv_nfold: no visible global function definition for ‘predict’
cv_nfold: no visible global function definition for ‘cv.glmnet’
cv_nfold: no visible global function definition for ‘coef’
cv_nfold: no visible global function definition for ‘var’
getoptbinsize: no visible global function definition for ‘var’
getoptbinsize: no visible global function definition for ‘cor’
glmcvbeta: no visible global function definition for ‘cv.glmnet’
myhistplot: no visible global function definition for ‘par’
myhistplot: no visible global function definition for ‘plot’
myhistplot: no visible global function definition for ‘axis’
plot.binmod: no visible global function definition for ‘par’
plot.binmod: no visible global function definition for ‘layout’
plot.binmod: no visible global function definition for ‘dev.off’
plot.binmod: no visible binding for global variable ‘plot.new’
plot.binmod: no visible global function definition for ‘postscript’
plot.binmod: no visible global function definition for ‘plot’
plot.binmod: no visible global function definition for ‘mtext’
plot.binmod: no visible global function definition for ‘legend’
plot.binmod: no visible global function definition for ‘arrows’
predict.binmod: no visible global function definition for ‘predict’
singlemarkanalysis: no visible global function definition for ‘glm’
singlemarkanalysis: no visible global function definition for ‘var’
weightedx: no visible global function definition for ‘na.exclude’
Undefined global functions or variables:
  arrows axis coef cor cv.glmnet dev.off glm layout legend mtext
  na.exclude par plot plot.new postscript predict var
Consider adding
  importFrom("grDevices", "dev.off", "postscript")
  importFrom("graphics", "arrows", "axis", "layout", "legend", "mtext",
             "par", "plot", "plot.new")
  importFrom("stats", "coef", "cor", "glm", "na.exclude", "predict",
             "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Vignette 'Japanese.Rnw' requires 'uplatex' and 'dvipdfmx'
Error: processing vignette 'Japanese.Rnw' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘patchDVI::JSweave’) for vignette with name ‘Japanese’. The following files exist in directory ‘.’: ‘Japanese.Rnw’, ‘patchDVI.Rnw’, ‘patchDVI.bib’, ‘sample.Rnw.txt’
Execution halted
Error in re-building vignettes:
  ...

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

Error: processing vignette 'pathClass.rnw' failed with diagnostics:
 chunk 2 (label = loadALLpackage) 
Error in library(golubEsets) : there is no package called ‘golubEsets’
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pbdMPI.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pbdPROF.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: pbkrtest
Loading required package: lme4
Loading required package: Matrix
refitting model(s) with ML (instead of REML)
refitting model(s) with ML (instead of REML)
   [[ suppressing 10 column names '1', '2', '3' ... ]]
   [[ suppressing 10 column names '1', '2', '3' ... ]]
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pbkrtest-introduction.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [noae]{Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   2.7Mb
    libs      1.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/pcaL1.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   5.9Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs    5.6Mb
    share  11.9Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
large z may result in inaccurate quantiles
Loading required package: polynom
Loading required package: reshape2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PDQutils.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘georob’ ‘spsurvey’
Packages unavailable to check Rd xrefs: ‘spsurvey’, ‘georob’
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Package suggested but not available for checking: ‘globaltest’
Errors in running code in vignettes:
when running code in ‘penalized.Rnw’
  ...

> fit <- penalized(response, X, lambda1 = 2, lambda2 = 2, 
+     fusedl = chr)


> library(globaltest)

  When sourcing ‘penalized.R’:
Error: there is no package called ‘globaltest’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: survival
Welcome to penalized. For extended examples, see vignette("penalized").

Error: processing vignette 'penalized.Rnw' failed with diagnostics:
 chunk 31 (label = globaltest) 
Error in library(globaltest) : there is no package called ‘globaltest’
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Paper_Analysis.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.5 \usepackage
               {tikz}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/permGPU.Rcheck/00install.out’ for details.
fbins: no visible global function definition for ‘quantile’
fhat: no visible global function definition for ‘dnorm’
fhatgg: no visible global function definition for ‘dnorm’
fhatnew: no visible global function definition for ‘dnorm’
mica: no visible global function definition for ‘cor’
trans: no visible binding for global variable ‘sd’
weight.seq: no visible global function definition for ‘dnorm’
weight.seq: no visible global function definition for ‘nlm’
Undefined global functions or variables:
  cor dnorm nlm quantile sd
Consider adding
  importFrom("stats", "cor", "dnorm", "nlm", "quantile", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: gsl
Loading required package: R2Cuba
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pgs_user.tex' failed.
LaTeX errors:
! LaTeX Error: File `path.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {listings}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘BiocParallel’
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd25d5338f2b1.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd25d5338f2b1.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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 48-53 (LongPhyloinfer.Rmd) 
Error: processing vignette 'LongPhyloinfer.Rmd' failed with diagnostics:
INLA needed for this function to work. Use install.packages("INLA", repos="https://www.math.ntnu.no/inla/R/stable").
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Error in re-building vignettes:
  ...
Attaching package: ‘R.oo’

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

Loading required package: ape
Loading required package: compoisson
Loading required package: MASS
Loading required package: ggplot2
Warning in setEquDist.GeneralSubstitution(this, value, force = TRUE) :
  The provided probabilities have been rescaled in order to sum to one!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!

Warning in insertSequence.Sequence(sequence, insert, insert.pos, process = process) :
  The length of the sequence to be inserted is zero! Nothing to do here!


Execution halted
Package required but not available: ‘qvalue’

Package suggested but not available for checking: ‘OCplus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘RPostgreSQL’ ‘topicmodels’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pivotalr.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.98 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshotb739448a5672.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb739448a5672.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
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq’
Error in re-building vignettes:
  ...
Saving an object of class 'gstatModel'...
Subsetting observations to fit the prediction domain in 2D...
Generating predictions using the trend model (RK method)...
Running 5-fold cross validation using 'krige.cv'...
Creating an object of class "SpatialPredictions"
KML file opened for writing...
Reprojecting to +proj=longlat +datum=WGS84 ...
Writing to KML...
Closing  fmd_ST.kml
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss1079.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.53 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘mvabund’
Error in re-building vignettes:
  ...

Attaching package: ‘pls’

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

    loadings

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pls-manual.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.7Mb
Error in re-building vignettes:
  ...
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
Warning in fitContinuous(phy = att$cache$phy, model = att$model, ..., ncores = 1) :
  Parameter estimates appear at bounds:
	lambda
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.

Execution halted
Package required but not available: ‘gWidgetsRGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘dplR’
as.popgraph: no visible global function definition for ‘is’
centroid_distance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘is’
centroid_variance: no visible global function definition for ‘cov’
decorate_graph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘is’
overlay_popgraph: no visible global function definition for ‘lines’
overlay_popgraph: no visible global function definition for ‘points’
overlay_popgraph: no visible global function definition for ‘text’
permute_popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘is’
popgraph: no visible global function definition for ‘qchisq’
popgraph: no visible global function definition for ‘prcomp’
popgraph: no visible global function definition for ‘var’
read.popgraph: no visible global function definition for ‘read.table’
test_congruence: no visible global function definition for ‘cor.test’
to_data.frame: no visible global function definition for ‘is’
to_pgraph: no visible global function definition for ‘is’
write_popgraph: no visible global function definition for ‘is’
write_popgraph : <anonymous>: no visible global function definition for
  ‘write.csv’
Undefined global functions or variables:
  cor.test cov is lines points prcomp qchisq read.table text var
  write.csv
Consider adding
  importFrom("graphics", "lines", "points", "text")
  importFrom("methods", "is")
  importFrom("stats", "cor.test", "cov", "prcomp", "qchisq", "var")
  importFrom("utils", "read.table", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Popgraph.tex’
Package has no Sweave vignette sources and no VignetteBuilder field.
Package suggested but not available for checking: ‘lfa’
Error in re-building vignettes:
  ...
Loading required package: boot
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'popKorn.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0  1.6844357  0.53539884          2     F
 9            9         9    20      1  0.9113913 -0.55527835          2     F
10           10        10    12      1  0.2374303  1.77950291          1     M
# ... with more rows

> library(VariantAnnotation)

  When sourcing ‘poplite.R’:
Error: there is no package called ‘VariantAnnotation’
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectEstim.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'PortfolioEffectHFT.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.15 \usepackage
                {setspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "loglik",  :
  For  loglik calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AIC",  :
  For  AIC calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in FUN(X[[i]], ...) : end value not changed
Warning in analyseMCMCs(object$fitMCMC$chains, stat = NULL, statName = "AICc",  :
  For  AICc calling coda::effectiveSize resulted in an error: Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 
  0 (non-NA) cases

Quitting from lines 419-430 (UserGuide.Rmd) 
Error: processing vignette 'UserGuide.Rmd' failed with diagnostics:
package 'Rmpfr' not found
Execution halted
Found the following significant warnings:
  powell.c:700:14: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
  powell.c:724:12: warning: format string is not a string literal (potentially insecure) [-Wformat-security]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/powell.Rcheck/00install.out’ for details.
File ‘powell/libs/powell.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Object: ‘powell.o’
  Found ‘_puts’, possibly from ‘printf’ (C), ‘puts’ (C)
    Object: ‘powell.o’

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

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

Packages which this enhances but not available for checking:
  ‘KEGG.db’ ‘org.Hs.eg.db’ ‘org.Sc.sgd.db’ ‘org.Ag.eg.db’
  ‘org.Pt.eg.db’ ‘org.Rn.eg.db’ ‘org.Ss.eg.db’ ‘org.At.tair.db’
  ‘org.Bt.eg.db’ ‘org.Ce.eg.db’ ‘org.Cf.eg.db’ ‘org.Dm.eg.db’
  ‘org.Dr.eg.db’ ‘org.EcK12.eg.db’ ‘org.EcSakai.eg.db’ ‘org.Gg.eg.db’
  ‘org.Mm.eg.db’ ‘org.Mmu.eg.db’ ‘org.Pf.plasmo.db’ ‘org.Xl.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Package suggested but not available for checking: ‘PerfMeas’
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘stats’
  All declared Imports should be used.
bias.correct.curve: no visible global function definition for ‘approx’
lines.principal.curve: no visible global function definition for
  ‘lines’
periodic.lowess: no visible global function definition for ‘lowess’
periodic.lowess: no visible global function definition for ‘approx’
plot.principal.curve: no visible global function definition for ‘plot’
points.principal.curve: no visible global function definition for
  ‘points’
principal.curve : <anonymous>: no visible global function definition
  for ‘lowess’
principal.curve : <anonymous>: no visible global function definition
  for ‘smooth.spline’
principal.curve : <anonymous>: no visible global function definition
  for ‘predict’
principal.curve: no visible global function definition for ‘var’
principal.curve: no visible global function definition for ‘plot’
principal.curve: no visible global function definition for ‘lines’
Undefined global functions or variables:
  approx lines lowess plot points predict smooth.spline var
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "approx", "lowess", "predict", "smooth.spline",
             "var")
to your NAMESPACE file.
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'charfunc.tex' failed.
LaTeX errors:
! LaTeX Error: File `esint.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'profdpm.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \newcommand
                {\bz}{\boldsymbol{z}}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.1Mb
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
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 71-76 (ProliferativeIndexVignette.Rmd) 
Error: processing vignette 'ProliferativeIndexVignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
  In `d' `NA' elements were replaced with string "NA"
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in `[<-.factor`(`*tmp*`, thisvar, value = "NA") :
  invalid factor level, NA generated
Warning in location(g3, species = c("human"), vertex.size = 3, vertex.label.cex = 0.5,  :
  There are some 'NA' values in graph attribute 'category'!
Warning in if (layout %in% c("reingold.tilford", "circle", "random", "fruchterman.reingold",  :
  the condition has length > 1 and only the first element will be used
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               {caption}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running ‘testthat.R’ [74s/75s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                  ^
  In file included from file3161620893c0.cpp:8:
  In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/StanHeaders/include/stan/math.hpp:4:
  In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/StanHeaders/include/stan/math/rev/mat.hpp:12:
  In file included from /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/StanHeaders/include/stan/math/prim/mat.hpp:58:
  /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.4/StanHeaders/include/stan/math/prim/mat/fun/autocorrelation.hpp:17:14: warning: function 'fft_next_good_size' is not needed and will not be emitted [-Wunneeded-internal-declaration]
        size_t fft_next_good_size(size_t N) {
               ^
  22 warnings generated.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 330 SKIPPED: 0 FAILED: 1
  1. Error: logistic_floor (@test_prophet.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Loading required package: RcppArmadillo
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'prospectr-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `authblk.sty' not found.

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

! Emergency stop.
<read *> 
         
l.65 \usepackage
                [cm, headings]{fullpage} % for larger margins^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘Biostrings’ ‘GOSemSim’ ‘org.Hs.eg.db’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.7Mb
Package suggested but not available for checking: ‘fftw’
Error in re-building vignettes:
  ...
Loading required package: Formula
Loading required package: ggplot2

Attaching package: ‘Hmisc’

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

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

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

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

! Emergency stop.
<read *> 
         
l.8 \definecolor
                {shadecolor}{rgb}{0.9, 0.9, 0.9}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘printr’
Namespaces in Imports field not imported from:
  ‘BayesFactor’ ‘methods’ ‘pbkrtest’
  All declared Imports should be used.
Running ‘testthat.R’ [52s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   Elapsed Time: 0.196686 seconds (Warm-up)
                 0.332192 seconds (Sampling)
                 0.528878 seconds (Total)
  
  .0%
  .33%
  .67%
  .100%
  1
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 97 SKIPPED: 0 FAILED: 1
  1. Failure: If it works. (@test-analyze.stanreg.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
    last_plot

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

    get_x, get_y

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

    filter

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

    layout

We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/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]="./webshot3f4769d322fc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot3f4769d322fc.png': No such file or directory
Quitting from lines 503-531 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Running ‘testthat.R’ [43s/44s]
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) : 78 | 77.7 | 79.7 (2)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 252 SKIPPED: 0 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#39) 
  2. Failure: createReport (@test_computeQC.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QGglmmHowTo.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.16 \usepackage
                {fancyhdr}		%En-tête personnalisés (voir \fancyhead)^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘GenomicFeatures’ ‘Rsamtools’ ‘exomePeak’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: replacing previous import ‘graphics::matplot’ by ‘fda::matplot’ when loading ‘QRFCCA’
  Warning: replacing previous import ‘stats::decompose’ by ‘igraph::decompose’ when loading ‘QRFCCA’
  Warning: replacing previous import ‘stats::spectrum’ by ‘igraph::spectrum’ when loading ‘QRFCCA’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/QRFCCA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/qtbase.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.2Mb
Error in re-building vignettes:
  ...
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Warning in `[<-`(`*tmp*`, i, value = <S4 object of class "taguchiFactor">) :
  implicit list embedding of S4 objects is deprecated
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qualityTools.tex' failed.
LaTeX errors:
! LaTeX Error: File `relsize.sty' not found.

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

! Emergency stop.
<read *> 
         
l.23 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/QuasiSeq.Rcheck/00install.out’ for details.
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Quipu_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `sectsty.sty' not found.

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

! Emergency stop.
<read *> 
         
l.31 \sectionfont
                 {\sffamily\bfseries\color{BiocBlue}\sectionrule{0pt}{0pt}{-...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
conf.statement: no visible global function definition for ‘pbeta’
Undefined global functions or variables:
  pbeta
Consider adding
  importFrom("stats", "pbeta")
to your NAMESPACE file.
Running ‘loadlibs.r’ [0s/1s]
  Running ‘test.r’ [1s/1s]
Running the tests in ‘tests/test.r’ failed.
Last 13 lines of output:
  > source('loadlibs.r')
  > loadlibs(forcelocal=TRUE)
  
  Attaching package: 'combinat'
  
  The following object is masked from 'package:utils':
  
      combn
  
  make: *** No rule to make target `../src/core.o', needed by `../src/Quor.so'.  Stop.
  Error in dyn.load(file.path(package.loc, "src", "Quor.so")) : 
    unable to load shared object '/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so':
    dlopen(/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Quor.Rcheck/tests/../src/Quor.so, 6): image not found
  Calls: loadlibs -> dyn.load
  Execution halted
File ‘qVarSel/libs/qVarSel.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘qVarSelH.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘qVarSelH.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'QZ-guide.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.72 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required but not available:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘AlgDesign’ ‘psych’
  All declared Imports should be used.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
Package suggested but not available for checking: ‘KEGGgraph’
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Error in re-building vignettes:
  ...
Loading required package: MASS
Loading required package: pcaPP
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rainbow.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    htmlwidgets   6.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Warning in rq.fit.br(wx, wy, tau = tau, ...) :
  Solution may be nonunique
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.23 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'random-essay.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \setpapersize
                 {USletter}                 % use USletter paper^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘rgeos’ ‘rgdal’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RanglaPunjab.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rankcluster.tex' failed.
LaTeX errors:
! LaTeX Error: File `elsarticle.cls' not found.

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

! Emergency stop.
<read *> 
         
l.4 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
http://code.google.com/p/pbs-software/

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RapidPolygonLookup.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RAppArmor.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   1.5Mb
Packages required but not available: ‘RGtk2’ ‘cairoDevice’

Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2Extras’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
Packages required but not available: ‘fmcsR’ ‘ChemmineR’ ‘KEGGREST’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   3.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Package suggested but not available for checking: ‘downscale’
Packages suggested but not available for checking: ‘git2r’ ‘devtools’
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
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 336-337 (RClone_qmsevpops.Rmd) 
Error: processing vignette 'RClone_qmsevpops.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rclusterpp
Loading required package: Rcpp
Loading required package: RcppEigen
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rclusterpp.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \lstset
           {language=C++,basicstyle=\footnotesize\ttfamily}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘Rcmdr’ ‘seeg’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running ‘testthat.R’ [56s/89s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: asNamespace(ns)
  8: getNamespace(ns)
  9: tryCatch(loadNamespace(name), error = function(e) stop(e))
  10: tryCatchList(expr, classes, parentenv, handlers)
  11: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  12: value[[3L]](cond)
  
  testthat results ================================================================
  OK: 742 SKIPPED: 32 FAILED: 3
  1. Error: loadCMIP5 handles spatial mismatches between ensembles (@test_loadCMIP5.R#104) 
  2. Error: loadCMIP5 handles FUN correctly (@test_loadCMIP5.R#193) 
  3. Error: loadEnsemble handles no files found (@test_loadEnsemble.R#35) 
  
  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/3.4/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    include   5.3Mb
    libs      1.6Mb
Running ‘doRUnit.R’ [100s/101s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
  test.as.dgr2dgc: (5 checks) ... OK (0.01 seconds)
  test.as.dgt2dgc: (18 checks) ... OK (0.11 seconds)
  test.as.dsc2dgc: (8 checks) ... OK (0.16 seconds)
  test.as.dsr2dgc: (4 checks) ... OK (0.03 seconds)
  test.as.dst2dgc: (2 checks) ... OK (0.01 seconds)
  test.as.dtc2dgc: (5 checks) ... OK (0.07 seconds)
  test.as.dtr2dgc: (4 checks) ... OK (0.02 seconds)
  test.as.dtt2dgc: (4 checks) ... OK (0.04 seconds)
  test.as.ind2dgc: (9 checks) ... OK (0.05 seconds)
  test.as.p2dgc: (5 checks) ... OK (0.02 seconds)
  test.as.stm2dgc: (1 checks) ... OK (0 seconds)
  test.as.stm2stm: (1 checks) ... OK (0.02 seconds)
  test.stop: (7 checks) ... OK (0.05 seconds)
  Error: TEST HAD ERRORS!
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Timing stopped at: 0.009 0 0.009
Error in spmat$getformat : $ operator not defined for this S4 class
Error : Only CSC, COO and CSR matrices from SciPy are supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(lm) : lgCMatrix is not supported.
Error in asSpMat(L) : lgTMatrix is not supported.
dimnames(.) <- NULL:  translated to 
dimnames(.) <- list(NULL,NULL)  <==>  unname(.)
Error in asSpMat(nm) : ngCMatrix is not supported.
Error in asSpMat(ngt) : ngTMatrix is not supported.
Error in asSpMat(nM) : ntTMatrix is not supported.
Error in asSpMat(nsc) : nsCMatrix is not supported.
Error in asSpMat(ldi) : ldiMatrix is not supported.

Error: processing vignette 'RcppArmadillo-unitTests.Rnw' failed with diagnostics:
 chunk 2 (label = unitTesting) 
Error in eval(expr, .GlobalEnv) : unit test problems: 1 errors
Execution halted
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppClassicExamples.Rcheck/00install.out’ for details.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.9Mb
installed size is 31.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.7Mb
    libs      7.9Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppMLPACK-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \usepackage
                {epstopdf}^^M
!  ==> 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:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppOctave.Rcheck/00install.out’ for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.4Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.2Mb
    libs      4.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppRedis.Rcheck/00install.out’ for details.
get_rollit_source: no visible global function definition for
  ‘file.edit’
Undefined global functions or variables:
  file.edit
Consider adding
  importFrom("utils", "file.edit")
to your NAMESPACE file.
installed size is 76.8Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      48.9Mb
    libs     23.4Mb
installed size is  5.1Mb
  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/3.4/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rcrypt.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘vcr’
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("rdatacite")
  Loading required package: rdatacite
  Error in library("vcr") : there is no package called 'vcr'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rDEA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RDieHarder.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error in re-building vignettes:
  ...
Loading required package: rDNAse
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rDNAse.tex' failed.
LaTeX errors:
! LaTeX Error: File `tablefootnote.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotc7f911e7adfb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc7f911e7adfb.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.0Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'readJDX.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.68 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  13.8Mb
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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
    lapply, lengths, mapply, match, mget, order, paste, pmax, pmax.int,
    pmin, pmin.int, rank, rbind, rowMeans, rowSums, rownames, sapply,
    setdiff, sort, table, tapply, union, unique, unsplit, which,
    which.max, which.min

Loading required package: grid

Error: processing vignette 'relations.Rnw' failed with diagnostics:
 chunk 26 (label = consensus1b) 
Error in loadNamespace(name) : there is no package called ‘Rglpk’
Execution halted
Packages in Depends field not imported from:
  ‘plyr’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': ‘Hmisc:::label.default’
  See the note in ?`:::` about the use of this operator.
S3 methods shown with full name in documentation object 'as.data.frame.correlation':
  ‘as.data.frame.correlation’

S3 methods shown with full name in documentation object 'as.data.frame.freq':
  ‘as.data.frame.freq’

S3 methods shown with full name in documentation object 'as.data.frame.summarize':
  ‘as.data.frame.summarize’

S3 methods shown with full name in documentation object 'as.data.frame.summarize.by':
  ‘as.data.frame.summarize.by’

S3 methods shown with full name in documentation object 'as.data.frame.survival':
  ‘as.data.frame.survival’

S3 methods shown with full name in documentation object 'as.data.frame.tabular':
  ‘as.data.frame.tabular’

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 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
MakeHierarchyTree: no visible global function definition for
  ‘as.formula’
Undefined global functions or variables:
  as.formula
Consider adding
  importFrom("stats", "as.formula")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Residuals numerically 0 are replaced by 1e-8
Warning in hglm.default(y = Y, X = X, Z = Z, RandC = RandC, maxit = 200,  :
  Hat-values numerically 1 are replaced by 1 - 1e-8
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RepeatABEL_vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Running ‘testthat.R’ [4s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 7
  1. Error: (unknown) (@test-docx-bookmarks.R#4) 
  2. Error: (unknown) (@test-docx-img.R#8) 
  3. Error: (unknown) (@test-docx-plot.R#10) 
  4. Error: (unknown) (@test-file-extensions.R#3) 
  5. Error: (unknown) (@test-flextable.R#30) 
  6. Error: (unknown) (@test-pptx-img.R#9) 
  7. Error: (unknown) (@test-pptx-plot.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 25 SKIPPED: 0 FAILED: 26
  1. Error: can't see environment of caller (@test-env.R#5) 
  2. Error: reprex doesn't write into environment of caller (@test-env.R#11) 
  3. Error: I understand exactly what I'm putting in reprex env (@test-env.R#22) 
  4. Error: reprex: expression input works (@test-input.R#17) 
  5. Error: reprex: character input works (@test-input.R#23) 
  6. Error: reprex: file input works (@test-input.R#31) 
  7. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  8. Error: Circular use is detected before render (@test-input.R#47) 
  9. Error: Leading prompts are removed (@test-input.R#55) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rsolr’
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘Guide_restorepoint.Rmd’, ‘Guide_restorepoint.html’,
    ‘Guide_restorepoint.md’
Package has no Sweave vignette sources and no VignetteBuilder field.
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RESTguide.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.63 \usepackage
                {float}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 27.1Mb
  sub-directories of 1Mb or more:
    libs  26.2Mb
Package required but not available: ‘PKI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    libs      77.2Mb
    pictures   1.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgeolocate.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rglpk.Rcheck/00install.out’ for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    3.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rgnuplot.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rrules’
Error in re-building vignettes:
  ...
(./tufte-handout.cls
Document Class: tufte-handout 2009/12/11 v3.5.0 Tufte-handout class
(./tufte-common.def
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/xkeyval/xkeyval.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkeyval.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/xkvutils.tex
(/usr/local/texlive/2016basic/texmf-dist/tex/generic/xkeyval/keyval.tex))))

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

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

Enter file name: 
! Emergency stop.
<read *> 
         
l.14 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Transcript written on rgp_introduction.log.
make: *** [pdf] Error 1
Error in buildVignettes(dir = "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rgp.Rcheck/vign_test/rgp") : 
  running 'make' failed
Execution halted
.onAttach: no visible global function definition for ‘sessionInfo’
rescaleIndividual: no visible global function definition for ‘cov’
rescaleIndividual: no visible global function definition for ‘var’
server: no visible global function definition for ‘read.csv’
server: no visible global function definition for ‘tail’
server: no visible global function definition for ‘as.formula’
server: no visible global function definition for ‘terms’
server: no visible global function definition for ‘plot’
server: no visible global function definition for ‘legend’
server: no visible global function definition for ‘lines’
server: no visible global function definition for ‘par’
server: no visible global function definition for ‘layout’
server: no visible global function definition for ‘points’
server: no visible global function definition for ‘barplot’
workerProcessRun: no visible global function definition for
  ‘as.formula’
workerProcessRun : <anonymous>: no visible global function definition
  for ‘runif’
workerProcessRun : progressMonitor: no visible global function
  definition for ‘alarm’
workerProcessRun : progressMonitor: no visible global function
  definition for ‘runif’
Undefined global functions or variables:
  alarm as.formula barplot cov layout legend lines par plot points
  read.csv runif sessionInfo tail terms var
Consider adding
  importFrom("graphics", "barplot", "layout", "legend", "lines", "par",
             "plot", "points")
  importFrom("stats", "as.formula", "cov", "runif", "terms", "var")
  importFrom("utils", "alarm", "read.csv", "sessionInfo", "tail")
to your NAMESPACE file.
Packages suggested but not available for checking:
  ‘graph’ ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’
  ‘rgdal’ ‘rggobi’ ‘Rgraphviz’ ‘SVGAnnotation’
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.4Mb
Namespace in Imports field not imported from: ‘RcppGSL’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: multiple methods tables found for ‘dbQuoteLiteral’
  Warning: replacing previous import ‘DBI::dbQuoteLiteral’ by ‘RPostgres::dbQuoteLiteral’ when loading ‘RGreenplum’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RGreenplum.Rcheck/00install.out’ for details.
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

> ### Name: grmod
> ### Title: Interface for _gretl_ estimation commands
> ### Aliases: grmod
> 
> ### ** Examples
> 
> set.seed(13)
> dfr = data.frame(y = rnorm(20), x = rnorm(20))
> grmod("ols y 0 x --simple-print",dfr)

No valid gretl executable: no output is produced
Error: '/tmp/RtmpGoPzuG/mbundlea2f6198a06bd.xml' does not exist.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rhosp.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {amsfonts,amsmath,amssymb,amsthm}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rhpc.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor the system RNG.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘rggobi’ ‘fftw’
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Running ‘test-all.R’ [1s/1s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library("testthat")
  > test_check("ritis")
  Loading required package: ritis
  
  Attaching package: 'ritis'
  
  The following object is masked from 'package:stats':
  
      terms
  
  Error in library("vcr") : there is no package called 'vcr'
  Calls: test_check ... source_dir -> lapply -> FUN -> eval -> eval -> library
  Execution halted
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rkafka.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following apparent object files/libraries:
  src/l64/c.o src/m64/c.o src/w32/c.o src/w64/c.o
Object files/libraries should not be included in a source package.
Found the following executable file:
  src/w32/c.o
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 45.1Mb
  sub-directories of 1Mb or more:
    exe  45.0Mb
Namespaces in Imports field not imported from:
  ‘Matrix’ ‘arules’ ‘pmml’ ‘rJava’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘genefilter’ ‘golubEsets’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package unavailable to check Rd xrefs: ‘rgdal’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rLindo.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
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/3.4/RMark.Rcheck/00install.out’ for details.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RmecabKo.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'The_rmgarch_models.tex' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [round]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
Execution halted
Running ‘RMongo-Ex.R’ [3s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck -> .Call
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rmpi.Rcheck/00install.out’ for details.
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rmweather)
  > 
  > test_check("rmweather")
  ── 1. Failure: Test training function (@test_02_rmw_functions.R#53)  ───────────
  model$r.squared not equal to 0.4184627.
  1/1 mismatches
  [1] 0.399 - 0.418 == -0.0196
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 1
  1. Failure: Test training function (@test_02_rmw_functions.R#53) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘topGO’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
Packages required but not available: ‘rgeos’ ‘rgdal’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
installed size is 93.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     91.1Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Error in re-building vignettes:
  ...
Loading required package: rgenoud
##  rgenoud (Version 5.7-12.4, Build Date: 2015-07-19)
##  See http://sekhon.berkeley.edu/rgenoud for additional documentation.
##  Please cite software as:
##   Walter Mebane, Jr. and Jasjeet S. Sekhon. 2011.
##   ``Genetic Optimization Using Derivatives: The rgenoud package for R.''
##   Journal of Statistical Software, 42(11): 1-26. 
##

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {thumbpdf,lmodern}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
cluster_em_outlier: no visible global function definition for ‘qchisq’
jth_dsty: no visible global function definition for ‘mahalanobis’
k_means: no visible global function definition for ‘kmeans’
mix_rcm: no visible global function definition for ‘median’
Undefined global functions or variables:
  kmeans mahalanobis median qchisq
Consider adding
  importFrom("stats", "kmeans", "mahalanobis", "median", "qchisq")
to your NAMESPACE file.
installed size is 30.4Mb
  sub-directories of 1Mb or more:
    libs  29.6Mb
Running ‘test_netlib.R’ [18s/30s]
Running the tests in ‘tests/test_netlib.R’ failed.
Last 13 lines of output:
  wood1p    1.442902e+00
  woodw     1.304476e+00
  > afiro <- netlib("afiro")
  > 
  > if ( length(ROI_applicable_solvers(afiro)) ) {
  + 	## solve a problem
  + 	sol <- ROI_solve(afiro)
  + 	sol
  + 	stopifnot( equal(sol$objval, 
  + 		       as.numeric(netlib("metainfo")["afiro", "optimal_value"])) )
  + }
  Error in SOLVE(x, ROI_translate(control, solver)) : 
    the directions "<", "<=", ">" and ">=" can only be used in combination with the "free" cone! The constraints c(3, 4, 7, 8, 9, 10, 13, 14, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27) are inequality constraints but don`t belong to the "free" cone.
  Calls: ROI_solve -> SOLVE
  Execution halted
Packages suggested but not available for checking: ‘proj4’ ‘rgdal’
Error in re-building vignettes:
  ...
Warning in engine$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 21-27 (rollply.Rmd) 
Error: processing vignette 'rollply.Rmd' failed with diagnostics:
there is no package called 'proj4'
Execution halted
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/ROracle.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘cartography’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rotations-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.99 \usepackage
                {titletoc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package unavailable to check Rd xrefs: ‘devtools’
Running ‘testthat.R’ [9s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: getExportedValue(pkg, name)
  8: asNamespace(ns)
  9: getNamespace(ns)
  10: tryCatch(loadNamespace(name), error = function(e) stop(e))
  11: tryCatchList(expr, classes, parentenv, handlers)
  12: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  13: value[[3L]](cond)
  
  ?testthat results ================================================================
  OK: 484 SKIPPED: 0 FAILED: 2
  1. Error: can document eager data (@test-rd-data.R#7) 
  2. Error: can document lazy data (@test-rd-data.R#15) 
  
  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/3.4/rpanel.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rpg.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.6Mb
Files in the 'vignettes' directory but no files in 'inst/doc':
  ‘TNRSVignette.pdf’, ‘rPlantVignette.pdf’
Package has no Sweave vignette sources and no VignetteBuilder field.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   3.8Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    extdata  12.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rpoppler.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RRreg.Rcheck/00install.out’ for details.
File ‘RSAgeo/libs/RSAgeo.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘RSAc.o’, ‘lib.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RSAc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSAP.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RSclient.Rcheck/00install.out’ for details.
File ‘rscproxy/libs/rscproxy.so’:
  Found non-API calls to R: ‘R_DefParams’, ‘R_ReplDLLinit’,
    ‘R_SetParams’, ‘R_set_command_line_arguments’, ‘Rf_endEmbeddedR’,
    ‘Rf_initEmbeddedR’, ‘ptr_R_Busy’, ‘ptr_R_ReadConsole’,
    ‘ptr_R_WriteConsole’, ‘ptr_R_WriteConsoleEx’

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: ‘RSclient’
Note: information on .o files is not available
File ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/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 the system RNG.
The detected symbols are linked into the code but might come from
libraries and not actually be called.
Compiled code should not call non-API entry points in R.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
installed size is 47.1Mb
  sub-directories of 1Mb or more:
    libs  46.6Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 101.1Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs  96.8Mb
installed size is 240.8Mb
  sub-directories of 1Mb or more:
    libs  238.5Mb
rbing.O2: no visible global function definition for ‘runif’
rbing.O2: no visible global function definition for ‘rbeta’
rbing.O2: no visible global function definition for ‘rbinom’
rbing.Op: no visible global function definition for ‘rnorm’
rbing.Op: no visible global function definition for ‘rbinom’
rbing.Op: no visible global function definition for ‘runif’
rbmf.O2: no visible global function definition for ‘runif’
rmf.matrix: no visible global function definition for ‘runif’
rmf.vector: no visible global function definition for ‘rnorm’
rmf.vector: no visible global function definition for ‘rbinom’
rustiefel: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  rbeta rbinom rnorm runif
Consider adding
  importFrom("stats", "rbeta", "rbinom", "rnorm", "runif")
to your NAMESPACE file.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/rsurface.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Rsymphony.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.5Mb
    projects   2.5Mb
Installation failed.
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/Ruchardet.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Package which this enhances but not available for checking: ‘devtools’
installed size is 24.8Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 46.0Mb
  sub-directories of 1Mb or more:
    libs  45.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RVowpalWabbit.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘rworldmapFAQ.Rnw’
  ...
> mtext("Source: Andy South, The R Journal Vol. 3/1, June 2011", 
+     side = 1, line = -1)

> par(mai = c(0, 0, 0.2, 0), xaxs = "i", yaxs = "i")

> library(rgdal)

  When sourcing ‘rworldmapFAQ.R’:
Error: there is no package called ‘rgdal’
Execution halted
Error in re-building vignettes:
  ...
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
149 codes from your data successfully matched countries in the map
0 codes from your data failed to match with a country code in the map
94 codes from the map weren't represented in your data
Warning in classInt::classIntervals(sPDF[["EPI"]], n = 5, style = "jenks") :
  var has missing values, omitted in finding classes
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rworldmap.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.37 \usepackage
                [colorlinks=true,urlcolor=blue]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs    4.8Mb
    yacas   1.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ryacas.tex' failed.
LaTeX errors:
! LaTeX Error: File `boxedminipage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 ^^M
       
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error in re-building vignettes:
  ...
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
`stat_bin()` using `bins = 30`. Pick better value with
`binwidth`.
large z may result in inaccurate quantiles
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sadists.tex' failed.
LaTeX errors:
! LaTeX Error: File `paralist.sty' not found.

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

! Emergency stop.
<read *> 
         
l.91 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: bbmle
Loading required package: stats4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sads_intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `framed.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {xspace}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘GO.db’ ‘GOstats’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sas7bdat.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.20     \usepackage
                    {Sweave}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'saves.tex' failed.
LaTeX errors:
! LaTeX Error: File `lastpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                [^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
plot.psgc: no visible global function definition for ‘par’
plot.psgc: no visible global function definition for ‘barplot’
plot.psgc: no visible global function definition for ‘hist’
plotci.sA: no visible global function definition for ‘par’
plotci.sA: no visible global function definition for ‘plot’
plotci.sA: no visible global function definition for ‘points’
plotci.sA: no visible global function definition for ‘segments’
plotci.sA: no visible global function definition for ‘abline’
plotci.sA: no visible global function definition for ‘axis’
qM.sM: no visible binding for global variable ‘quantile’
rwish: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘qnorm’
sbgcop.mcmc: no visible global function definition for ‘rnorm’
sbgcop.mcmc: no visible global function definition for ‘cov’
sbgcop.mcmc: no visible global function definition for ‘runif’
sbgcop.mcmc: no visible global function definition for ‘pnorm’
sbgcop.mcmc: no visible global function definition for ‘quantile’
summary.psgc: no visible global function definition for ‘acf’
Undefined global functions or variables:
  abline acf axis barplot cov hist par plot pnorm points qnorm quantile
  rnorm runif segments
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "hist", "par",
             "plot", "points", "segments")
  importFrom("stats", "acf", "cov", "pnorm", "qnorm", "quantile",
             "rnorm", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scaRabee.tex' failed.
LaTeX errors:
! LaTeX Error: File `ucs.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [latin1]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'scglrVignettes.tex' failed.
LaTeX errors:
! LaTeX Error: File `diagbox.sty' not found.

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

! Emergency stop.
<read *> 
         
l.64 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
futuresplot: no visible global function definition for ‘rainbow’
plot.schwartz2f.fit: no visible global function definition for
  ‘colorRampPalette’
plot.schwartz2f.fit: no visible global function definition for
  ‘rainbow’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘colorRampPalette’
plot,schwartz2f.fit-missing: no visible global function definition for
  ‘rainbow’
Undefined global functions or variables:
  colorRampPalette rainbow
Consider adding
  importFrom("grDevices", "colorRampPalette", "rainbow")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TechnicalDocument.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SciencesPo 1.4.1
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(names(TABLE)) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Warning: `panel.margin` is deprecated. Please use `panel.spacing` property instead
Warning: `legend.margin` must be specified using `margin()`. For the old behavior use legend.spacing
Quitting from lines 754-756 (Indices.Rmd) 
Error: processing vignette 'Indices.Rmd' failed with diagnostics:
there is no package called 'devtools'
Execution halted
Error in re-building vignettes:
  ...

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

Warning in i[, 2]/crossdist(start, end) :
  Recycling array of length 1 in vector-array arithmetic is deprecated.
  Use c() or as.vector() instead.

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

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {marginnote}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
plot.SK: no visible global function definition for ‘plot’
plot.SK: no visible global function definition for ‘segments’
plot.SK: no visible global function definition for ‘axis’
plot.SK: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis mtext plot segments
Consider adding
  importFrom("graphics", "axis", "mtext", "plot", "segments")
to your NAMESPACE file.
Package required but not available: ‘BiocParallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘oligoClasses’
Package suggested but not available for checking: ‘rgbif’
Error in re-building vignettes:
  ...
Loading required package: sp
[1] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio1.bil" 
[2] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio11.bil"
[3] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio12.bil"
[4] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio14.bil"
[5] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio16.bil"
[6] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio5.bil" 
[7] "/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdmvspecies.Rcheck/sdmvspecies/external/env/bio7.bil" 
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sdmvspecies.tex' failed.
LaTeX errors:
! LaTeX Error: File `hanging.sty' not found.

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

! Emergency stop.
<read *> 
         
l.9 \usepackage
               [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/sdols.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'doptimal.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithm.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {algpseudocode}% http://ctan.org/pkg/algorithmicx^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                [colorlinks = true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Preparing the data.
Fitting model for 04035.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304035.pdf.
Fitting model for 04041.
Computing the best seasonal wave.
Final model survreg results saved to myfit3_survregCall.txt.
Plots saved to myfit304041.pdf.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \hypersetup
               {^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages in Depends field not imported from:
  ‘car’ ‘sgeostat’ ‘spatstat’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...
Attaching package: ‘Ecfun’

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

    sign


Attaching package: ‘Ecdat’

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

    Orange

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'SeleMix-vignette.tex' failed.
BibTeX errors:
The top-level auxiliary file: SeleMix-vignette.aux
I couldn't open style file chicago.bst
---line 30 of file SeleMix-vignette.aux
 : \bibstyle{chicago
 :                  }
I'm skipping whatever remains of this command
I found no style file---while reading file SeleMix-vignette.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
      see ?specifyEquations
Loading required package: XML

Attaching package: 'XML'

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

    toHTML

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

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               [english]{babel}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'methodology.tex' failed.
LaTeX errors:
! LaTeX Error: File `algorithmic.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'seqDesignInstructions.tex' failed.
LaTeX errors:
! LaTeX Error: File `multirow.sty' not found.

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               [round,authoryear]{natbib}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs   6.1Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.ltx' failed with diagnostics:
Running 'texi2dvi' on 'vignette.ltx' failed.
LaTeX errors:
! LaTeX Error: File `beramono.sty' not found.

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

! Emergency stop.
<read *> 
         
l.7 \usepackage
               [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
installed size is 110.9Mb
  sub-directories of 1Mb or more:
    doc     10.8Mb
    libs    96.2Mb
    sqlite   1.5Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Malformed Description field: should contain one or more complete sentences.
Deprecated license: BSD
Packages in Depends field not imported from:
  ‘Matrix’ ‘fields’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
distLaplacian: no visible global function definition for ‘sparseMatrix’
gmdDeflation: no visible global function definition for ‘rnorm’
laplacian: no visible global function definition for ‘sparseMatrix’
Undefined global functions or variables:
  rnorm sparseMatrix
Consider adding
  importFrom("stats", "rnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sgt.tex' failed.
LaTeX errors:
! LaTeX Error: File `todonotes.sty' not found.

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

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

Cannot find a suitable Scala installation.

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

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

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

Cannot find a suitable Scala installation.

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

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

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

Cannot find a suitable Scala installation.

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

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

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

Cannot find a suitable Scala installation.

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

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

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

    summary

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

    summary

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

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

! Emergency stop.
<read *> 
         
l.72 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    www   6.4Mb
Error in re-building vignettes:
  ...

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

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

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

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

! Emergency stop.
<read *> 
         
l.80 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
plot.std: no visible global function definition for ‘rainbow’
plot.std: no visible global function definition for ‘legend’
read.std: no visible global function definition for ‘read.table’
std: no visible global function definition for ‘na.exclude’
Undefined global functions or variables:
  legend na.exclude rainbow read.table
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "legend")
  importFrom("stats", "na.exclude")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: Formula

Attaching package: 'Hmisc'

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

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

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

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                [utf8]{inputenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Found more than one class "indbasedModel" in cache; using the first, from namespace 'simecol'
Also defined by ‘.GlobalEnv’
Loading required package: FME
Loading required package: rootSolve
Loading required package: coda
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'b-simecol-howtos.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.58 \RequirePackage
                    [T1]{fontenc}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   9.5Mb
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg38’
Packages suggested but not available for checking: ‘Rmpi’ ‘copula’
Running ‘doExtras.R’ [1s/1s]
  Comparing ‘doExtras.Rout’ to ‘doExtras.Rout.save’ ... OK
  Running ‘getArray-swap.R’ [1s/2s]
  Running ‘tst-wrongs.R’ [16s/53s]
  Running ‘tstTGforecasts.R’ [5s/18s]
  Running ‘tstVaRsuperadd.R’ [1s/1s]
Running the tests in ‘tests/tstVaRsuperadd.R’ failed.
Last 13 lines of output:
  > ## manually
  > require(copula) # for the following call of doOne()
  Loading required package: copula
  
  > nonGr <- get.nonGrids(varList)$nonGrids
  
  > dd <- doOne(n= min(nonGr$n, 100), d=4, family="Clayton", tau=0.5,
  +             qmargin=nonGr$qmargin, alpha=nonGr$alpha)
  Error in onacopulaL("Clayton", list(th = iTau(archmCopula("clayton"),  : 
    could not find function "onacopulaL"
  Calls: demo -> source -> withVisible -> eval -> eval -> doOne
  In addition: Warning message:
  In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
    there is no package called 'copula'
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...

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

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

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

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

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

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

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

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

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

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

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

! Emergency stop.
<read *> 
         
l.4 \RequirePackage
                   {xcolor}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hitandrun’
Package unavailable to check Rd xrefs: ‘hitandrun’
Error in re-building vignettes:
  ...
Warning 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 123-124 (Report_r1.Rmd) 
Error: processing vignette 'Report_r1.Rmd' failed with diagnostics:
unused argument (options = list(eval = TRUE, echo = FALSE, results = "markup", tidy = FALSE, tidy.opts = NULL, collapse = FALSE, prompt = FALSE, comment = "##", highlight = TRUE, strip.white = TRUE, size = "normalsize", background = "#F7F7F7", cache = 0, cache.path = "cache/", cache.vars = NULL, cache.lazy = TRUE, dependson = NULL, autodep = FALSE, cache.rebuild = FALSE, fig.keep = "high", fig.show = "asis", fig.align = "default", fig.path = "figure/", dev = "png", dev.args = NULL, dpi = 72, fig.ext = "png", 
    fig.width = 7, fig.height = 7, fig.env = "figure", fig.cap = NULL, fig.scap = NULL, fig.lp = "fig:", fig.subcap = NULL, fig.pos = "", out.width = NULL, out.height = NULL, out.extra = NULL, fig.retina = 1, external = TRUE, sanitize = FALSE, interval = 1, aniopts = "controls,loop", warning = FALSE, error = FALSE, message = TRUE, render = list(Vname = 1:8, Group = c(1, 1, 1, 1, 1, 1, 1, 1), TN = c(400, 400, 400,
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smm.tex' failed.
LaTeX errors:
! LaTeX Error: File `enumitem.sty' not found.

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

! Emergency stop.
<read *> 
         
l.21 \usepackage
                {diagbox}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pairwiseSNHT.tex' failed.
LaTeX errors:
! LaTeX Error: File `breakurl.sty' not found.

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

! Emergency stop.
<read *> 
         
l.61 \usepackage
                {hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/soiltexture.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘meteoForecast’
Error in re-building vignettes:
  ...
Warning in FUN(X[[i]], ...) :
  swe:Quantity given without unit of measurement: Salinity

Attaching package: ‘xtable’

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

    label

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

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

! Emergency stop.
<read *> 
         
l.19 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’ ‘org.Hs.eg.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, cbind, colMeans, colSums, colnames, do.call,
    duplicated, eval, evalq, get, grep, grepl, intersect,
    is.unsorted, lapply, lengths, mapply, match, mget, order,
    paste, pmax, pmax.int, pmin, pmin.int, rank, rbind, rowMeans,
    rowSums, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min

Identifing all possible orderings..
Total run time: 1.19 secs
Identifing all possible orderings..
Total run time: 1.22 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc243394ccb72.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc243394ccb72.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
span: no visible global function definition for ‘complete.cases’
spanr: no visible global function definition for ‘model.frame’
spanr: no visible global function definition for ‘complete.cases’
spanr.hull: no visible global function definition for ‘par’
spanr.hull: no visible global function definition for ‘plot.new’
spanr.hull: no visible global function definition for ‘plot.window’
spanr.hull: no visible global function definition for ‘axis’
spanr.hull: no visible global function definition for ‘title’
spanr.hull: no visible global function definition for ‘points’
spanr.hull: no visible global function definition for ‘lines’
spanr.hull: no visible global function definition for ‘abline’
spanr.hull: no visible global function definition for ‘text’
spanr.hull: no visible global function definition for ‘segments’
spanr.hull: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box complete.cases lines model.frame par plot.new
  plot.window points segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "box", "lines", "par",
             "plot.new", "plot.window", "points", "segments", "text",
             "title")
  importFrom("stats", "complete.cases", "model.frame")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/spant.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotdcab656233c5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotdcab656233c5.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Clarketest: no visible global function definition for ‘pbinom’
Clarketest: no visible global function definition for ‘qbinom’
DIC: no visible global function definition for ‘model.matrix’
LogLike: no visible global function definition for ‘model.matrix’
Vuongtest: no visible global function definition for ‘var’
Vuongtest: no visible global function definition for ‘qnorm’
Vuongtest: no visible global function definition for ‘pnorm’
est.sc: no visible global function definition for ‘model.matrix’
gpind: no visible global function definition for ‘rgamma’
nbind: no visible global function definition for ‘rgamma’
poiind: no visible global function definition for ‘rgamma’
zigpind: no visible global function definition for ‘rbinom’
zigpind: no visible global function definition for ‘rgamma’
zipind: no visible global function definition for ‘rbinom’
zipind: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  model.matrix pbinom pnorm qbinom qnorm rbinom rgamma var
Consider adding
  importFrom("stats", "model.matrix", "pbinom", "pnorm", "qbinom",
             "qnorm", "rbinom", "rgamma", "var")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘moments’ ‘poweRlaw’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Loading required package: Matrix
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Replacing existing trend.
Smooth interpolated at 279 time(s).
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ST_tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `hyphenat.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                [unicode,linktocpage=true,bookmarksnumbered=true]{hyperref}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.7Mb
    help   5.1Mb
    libs   1.6Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  13.6Mb
Package required but not available: ‘MassSpecWavelet’

Package suggested but not available for checking: ‘speaq’

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

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

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

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

Attaching package: ‘spray’

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

    pmax, pmin

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

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

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

Version 3.3 of the spsurvey package was loaded successfully.

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

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

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

! Emergency stop.
<read *> 
         
l.7 \bibliographystyle
                      {chicago}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.3Mb
.GameSPT: no visible global function definition for ‘runif’
.GameSPT: no visible global function definition for ‘points’
.GameST: no visible global function definition for ‘runif’
.GameST: no visible global function definition for ‘points’
.arc: no visible global function definition for ‘lines’
.ptpedal: no visible global function definition for ‘polygon’
.sptpedal2: no visible global function definition for ‘segments’
.sptpedal3: no visible global function definition for ‘polygon’
.sptpedal4: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘plot’
chaos.spt: no visible global function definition for ‘polygon’
chaos.spt: no visible global function definition for ‘runif’
chaos.spt: no visible global function definition for ‘points’
chaos.st: no visible global function definition for ‘plot’
chaos.st: no visible global function definition for ‘polygon’
chaos.st: no visible global function definition for ‘runif’
chaos.st: no visible global function definition for ‘points’
plot.spt: no visible global function definition for ‘plot’
plot.spt: no visible global function definition for ‘polygon’
plot.st: no visible global function definition for ‘plot’
plot.st: no visible global function definition for ‘polygon’
Undefined global functions or variables:
  lines plot points polygon runif segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "polygon",
             "segments")
  importFrom("stats", "runif")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘RPostgreSQL’ ‘RODBC’
draw.srd: no visible global function definition for ‘complete.cases’
draw.srd: no visible global function definition for ‘runif’
draw.srd: no visible global function definition for ‘arrows’
draw.srd: no visible global function definition for ‘text’
draw.srd: no visible global function definition for ‘segments’
draw.srd.enc: no visible global function definition for ‘par’
draw.srd.enc: no visible global function definition for ‘plot.new’
draw.srd.enc: no visible global function definition for ‘plot.window’
draw.srd.enc: no visible global function definition for ‘rgb’
draw.srd.enc: no visible global function definition for ‘polygon’
draw.srd.enc: no visible global function definition for ‘pchisq’
draw.srd.enc: no visible global function definition for ‘text’
draw.srd.enc: no visible global function definition for ‘title’
draw.srd.enc: no visible global function definition for ‘arrows’
drawcell: no visible global function definition for ‘polygon’
drawcell: no visible global function definition for ‘segments’
rotate.srd: no visible global function definition for ‘devAskNewPage’
srd: no visible global function definition for ‘devAskNewPage’
Undefined global functions or variables:
  arrows complete.cases devAskNewPage par pchisq plot.new plot.window
  polygon rgb runif segments text title
Consider adding
  importFrom("grDevices", "devAskNewPage", "rgb")
  importFrom("graphics", "arrows", "par", "plot.new", "plot.window",
             "polygon", "segments", "text", "title")
  importFrom("stats", "complete.cases", "pchisq", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Loading required package: miscTools

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

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: spdep
Loading required package: sp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ssfavignette.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

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

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

! Emergency stop.
<read *> 
         
l.8 \usepackage
               {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
Packages suggested but not available for checking:
  ‘easyNCDF’ ‘s2dverification’
Unavailable namespace imported from by a ':::' call: ‘s2dverification’
  See the note in ?`:::` about the use of this operator.
Package unavailable to check Rd xrefs: ‘s2dverification’
Namespaces in Imports field not imported from:
  ‘magrittr’ ‘rpart’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: replacing previous import ‘igraph::dfs’ by ‘RBGL::dfs’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::transitivity’ by ‘RBGL::transitivity’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::bfs’ by ‘RBGL::bfs’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::decompose’ by ‘stats::decompose’ when loading ‘SteinerNet’
  Warning: replacing previous import ‘igraph::spectrum’ by ‘stats::spectrum’ when loading ‘SteinerNet’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SteinerNet.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
bos.cat2: no visible global function definition for ‘resid’
bos.cat2: no visible global function definition for ‘lm’
plot.rt: no visible global function definition for ‘plot’
plot.rt: no visible global function definition for ‘text’
plot.rt: no visible global function definition for ‘rect’
plot.rt: no visible global function definition for ‘title’
plot.rt: no visible global function definition for ‘par’
stdata: no visible binding for global variable ‘var’
stima: no visible global function definition for ‘fitted’
stima: no visible global function definition for ‘lm’
stima: no visible global function definition for ‘anova’
stima: no visible global function definition for ‘predict’
stima: no visible global function definition for ‘cor’
stima: no visible global function definition for ‘as.formula’
stima: no visible global function definition for ‘step’
Undefined global functions or variables:
  anova as.formula cor fitted lm par plot predict rect resid step text
  title var
Consider adding
  importFrom("graphics", "par", "plot", "rect", "text", "title")
  importFrom("stats", "anova", "as.formula", "cor", "fitted", "lm",
             "predict", "resid", "step", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amstext.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsgen.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsbsy.sty)
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsmath/amsopn.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amssymb.sty
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/amsfonts/amsfonts.sty))
(/usr/local/texlive/2016basic/texmf-dist/tex/latex/tools/bm.sty)

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

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

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=georgia&zoom=5&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=georgia&sensor=false
Warning: Removed 703 rows containing missing values (geom_point).
Warning: Removed 89 rows containing missing values (geom_point).
Warning: Removed 1 rows containing missing values (geom_path).
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 98-100 (Overview.Rmd) 
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
there is no package called 'tigris'
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
Namespace with empty importFrom: ‘tcltk2’
DetailOpLines: no visible global function definition for
  ‘tkProgressBar’
DetailOpLines: no visible global function definition for
  ‘setTkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘tkProgressBar’
MultiTrainWithInventory: no visible global function definition for
  ‘setTkProgressBar’
SimHistory: no visible global function definition for ‘tkProgressBar’
SimHistory: no visible global function definition for
  ‘setTkProgressBar’
Undefined global functions or variables:
  setTkProgressBar tkProgressBar
Error in re-building vignettes:
  ...
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
Running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed.
LaTeX errors:
! LaTeX Error: File `appendix.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Namespace in Imports field not imported from: ‘lwgeom’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning 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 111-114 (introducing-stplanr.Rmd) 
Error: processing vignette 'introducing-stplanr.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  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/3.4/StratSel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘limma’ ‘samr’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.9Mb
'library' or 'require' call to ‘ROAuth’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running ‘test-all.R’ [167s/242s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  RUNIT TEST PROTOCOL -- Mon Apr  3 00:44:25 2017 
  *********************************************** 
  Number of test functions: 18 
  Number of errors: 1 
  Number of failures: 0 
  
   
  1 Test Suite : 
  stremr unit testing - 18 test functions, 1 error, 0 failures
  ERROR in test.speedglm.allestimators10Kdata: Error in readChar(con, 5L, useBytes = TRUE) : cannot open the connection
  Error: 
  
  unit testing failed (#test failures: 0, #R errors: 1)
  
  Execution halted
Packages required but not available: ‘GO.db’ ‘biomaRt’ ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.4Mb
Package required but not available: ‘mutoss’

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: sandwich
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'strucchange-intro.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {graphicx,color,alltt}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘KFKSDS’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘genefilter’ ‘sva’
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/surrosurv.Rcheck/vign_test/surrosurv") :
  Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'copulas.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, natbib, hyperref, doi}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking:
  ‘graphite’ ‘curatedOvarianData’ ‘BiocStyle’ ‘org.Hs.eg.db’
Running ‘runTests.R’ [11s/11s]
Running the tests in ‘tests/runTests.R’ failed.
Last 13 lines of output:
  Test files with failing tests
  
     test_cliqueSurvivalTest.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_cliqueSurvivalTest.R 
  
     test_computePCs.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_computePCs.R 
  
     test_pathwaySurvivalTest.R 
       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/survClip.Rcheck/survClip/unitTests/test_pathwaySurvivalTest.R 
  
  
  Error in BiocGenerics:::testPackage("survClip") : 
    unit tests failed for package survClip
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.3Mb
installed size is 66.8Mb
  sub-directories of 1Mb or more:
    libs  66.1Mb
Package unavailable to check Rd xrefs: ‘survJamda’
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plots.tex' failed.
LaTeX errors:
! LaTeX Error: File `morefloats.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                [section]{placeins}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
lines.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘plot’
plot.survfitr: no visible global function definition for ‘lines’
plot.survfitr: no visible global function definition for ‘qnorm’
print.survfitr : pfun: no visible global function definition for
  ‘median’
survdiffr: no visible global function definition for ‘runif’
survdiffr: no visible global function definition for ‘terms’
survdiffr: no visible global function definition for ‘model.extract’
survfitr: no visible global function definition for ‘terms’
survfitr: no visible global function definition for ‘model.extract’
Undefined global functions or variables:
  lines median model.extract plot qnorm runif terms
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "median", "model.extract", "qnorm", "runif",
             "terms")
to your NAMESPACE file.
File ‘survrec/libs/survrec.so’:
  Found ‘__gfortran_rand’, possibly from ‘rand’ (Fortran)
    Object: ‘bootstrap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Loading required package: SurvRegCensCov
Loading required package: survival
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'weibull.tex' failed.
LaTeX errors:
! LaTeX Error: File `a4wide.sty' not found.

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

! Emergency stop.
<read *> 
         
l.3 \usepackage
               {amsmath, amsthm, amssymb}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'svUnit.tex' failed.
LaTeX errors:
! LaTeX Error: File `utf8x.def' not found.

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/XT3/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/SWATmodel.Rcheck/00install.out’ for details.