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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd25d5338f2b1.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd25d5338f2b1.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package in Depends field not imported from: ‘raster’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Error in re-building vignettes:
  ...
Warning in engine$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
plotData: no visible global function definition for ‘plot’
plotData: no visible global function definition for ‘abline’
plotData: no visible global function definition for ‘text’
Undefined global functions or variables:
  abline plot text
Consider adding
  importFrom("graphics", "abline", "plot", "text")
to your NAMESPACE file.
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
Running ‘testthat.R’ [19s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: CreatePackageReport(pkg_name = "baseballstats", report_path = testReportPath) at testthat/test-CreatePackageReport.R:19
  2: .RenderPackageReport(report_path = report_path, pkg_reporters = builtReporters, pkg_name = pkg_name)
  3: rmarkdown::render(system.file(file.path("package_report", "package_report.Rmd"), 
         package = "pkgnet"), output_file = report_path, quiet = TRUE, params = list(reporters = pkg_reporters, 
         pkg_name = pkg_name))
  4: pandoc_available(required_pandoc, error = TRUE)
  5: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 47 SKIPPED: 0 FAILED: 1
  1. Error: Test that CreatePackageReport Runs (@test-CreatePackageReport.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 60-95 (pkgnet-intro.Rmd) 
Error: processing vignette 'pkgnet-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
plot.burndown: no visible global function definition for ‘par’
plot.burndown: no visible global function definition for ‘hcl’
plot.burndown: no visible global function definition for ‘plot’
plot.burndown: no visible global function definition for ‘polygon’
plot.burndown: no visible global function definition for ‘lm’
plot.burndown: no visible global function definition for ‘abline’
plot.burndown: no visible global function definition for ‘lines’
plot.burndown: no visible global function definition for ‘points’
plot.burndown: no visible global function definition for ‘legend’
plot.burndown: no visible global function definition for ‘mtext’
plot.gantt: no visible global function definition for ‘gray’
plot.gantt: no visible global function definition for ‘par’
plot.gantt: no visible global function definition for ‘strheight’
plot.gantt: no visible global function definition for ‘strwidth’
plot.gantt: no visible global function definition for ‘plot’
plot.gantt: no visible global function definition for ‘box’
plot.gantt: no visible global function definition for ‘mtext’
plot.gantt: no visible global function definition for ‘axis.POSIXct’
plot.gantt: no visible global function definition for ‘rug’
plot.gantt: no visible global function definition for ‘abline’
plot.gantt: no visible global function definition for ‘axis’
plot.gantt: no visible global function definition for ‘lines’
plot.gantt: no visible global function definition for ‘rect’
Undefined global functions or variables:
  abline axis axis.POSIXct box gray hcl legend lines lm mtext par plot
  points polygon rect rug strheight strwidth
Consider adding
  importFrom("grDevices", "gray", "hcl")
  importFrom("graphics", "abline", "axis", "axis.POSIXct", "box",
             "legend", "lines", "mtext", "par", "plot", "points",
             "polygon", "rect", "rug", "strheight", "strwidth")
  importFrom("stats", "lm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in rug(subTics) : some values will be clipped
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'plan.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.11 \usepackage
                {boxedminipage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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:
  ...


Attaching package: 'gridExtra'

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

    combine

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

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.
Namespaces in Imports field not imported from:
  ‘Hmisc’ ‘digest’ ‘htmltools’ ‘knitr’ ‘lazyWeave’ ‘lubridate’ ‘rJava’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘polmineR.Rcpp’ ‘europarl.en’ ‘rcqp’
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
estMod.rinvGamma.mar29: no visible global function definition for
  ‘rgamma’
life.expectancy.stationary: no visible global function definition for
  ‘head’
life.expectancy.stationary: no visible global function definition for
  ‘tail’
log.lhood.mar29: no visible global function definition for ‘dnorm’
log.post.mar29: no visible global function definition for ‘dnorm’
popRecon.sampler: no visible global function definition for ‘rnorm’
popRecon.sampler: no visible global function definition for ‘runif’
Undefined global functions or variables:
  dnorm head rgamma rnorm runif tail
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm", "runif")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...

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

    object.size

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

    startsWith

Calculating life expectancy at birth ...
... done
Calculating net number of migrants ...
... done
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'burkina-faso-females.tex' failed.
BibTeX errors:
The top-level auxiliary file: burkina-faso-females.aux
I couldn't open style file apa.bst
---line 19 of file burkina-faso-females.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file burkina-faso-females.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 ‘custom_moments_objectives.Rnw’
  ...
+     r .... [TRUNCATED] 

> opt.sd <- optimize.portfolio(R, SD.portf, optimize_method = "ROI", 
+     momentFUN = "sigma.robust")
Loading required package: MASS

  When sourcing ‘custom_moments_objectives.R’:
Error: No solution found: Error in UseMethod("as.constraint") : 
  no applicable method for 'as.constraint' applied to an object of class "c('matrix', 'list')"
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 in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DesignThoughts.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.13 \usepackage
                {ctable}^^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 '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’
Running ‘testthat-prediction.R’ [26s/27s]
Running the tests in ‘tests/testthat-prediction.R’ failed.
Last 13 lines of output:
  no applicable method for 'predict' applied to an object of class "c('ksvm', 'vm')"
  1: prediction(m, data = genetrain) at testthat/tests-methods.R:255
  2: prediction.ksvm(m, data = genetrain)
  3: predict(model, newdata = out, type = "response", ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 164 SKIPPED: 0 FAILED: 5
  1. Error: Test prediction() for 'glimML' (@tests-methods.R#33) 
  2. Error: Test prediction() for 'glimQL' (@tests-methods.R#40) 
  3. Error: Test prediction() for 'gausspr' (@tests-methods.R#236) 
  4. Error: Test prediction() for 'kqr' (@tests-methods.R#244) 
  5. Error: Test prediction() for 'ksvm' (@tests-methods.R#255) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Package suggested but not available for checking: ‘prioritizr’
Namespaces in Imports field not imported from:
  ‘methods’ ‘utils’
  All declared Imports should be used.
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
File ‘processx/libs/processx.so’:
  Found non-API call to R: ‘R_new_custom_connection’

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 '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 ‘ProFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: profitBruteConv
> ### Title: Low level brute force image convolution
> ### Aliases: profitBruteConv
> ### Keywords: PSF convolve convolution
> 
> ### ** Examples
> 
> model = list(
+ 	sersic = list(
+ 		xcen   = c(180, 60),
+ 		ycen   = c(90, 10),
+ 		mag = c(15, 13),
+ 		re  = c(14, 5),
+ 		nser  = c(3, 10),
+ 		ang  = c(46, 80),
+ 		axrat  = c(0.4, 0.6),
+ 		box = c(0.5,-0.5)
+ 	)
+ )
> 
> model.image=profitMakeModel(model=model, dim=c(200,200))$z
> 
> # Without convolution:
> 
> magimage(model.image)

 *** caught segfault ***
address 0x60, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
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’ [54s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  Initial log joint probability = -15.5191
  Optimization terminated normally: 
    Convergence detected: relative gradient magnitude is below tolerance
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 230 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’
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) : 77.9 | 77.6 | 79.6 (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 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.7Mb
Namespace in Imports field not imported from: ‘lazyeval’
  All declared Imports should be used.
Missing or unexported object: ‘purrr::as_mapper’
Package required but not available: ‘Rmpfr’

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 '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
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
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
Package required but not available: ‘edgeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
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’
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.
Error in re-building vignettes:
  ...
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font width unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
Warning in text.default(xlim[1], 2, transcript, adj = 0, cex = 1.2) :
  font metrics unknown for character 0x9
[getGenePositions.ucscGenome] Adding 'start_codon' and 'stop_codon' positions.
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rbamtools.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.25 \usepackage
                {hyperref}                       % Index links, should be lo...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
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.
Loading required package: sp

Attaching package: 'dplyr'

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

    intersect, select, union

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 16-24 (BGM_Spatial.Rmd) 
Error: processing vignette 'BGM_Spatial.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
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:
  ‘orloca’ ‘orloca.es’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Rcmdr.new.loca.p: no visible binding for global variable ‘top’
Rcmdr.new.loca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.orloca.norm: no visible binding for global variable ‘top’
Rcmdr.orloca.norm : onOK: no visible binding for global variable
  ‘normaVariable’
Rcmdr.orloca.norm: no visible binding for global variable ‘normaFrame’
Rcmdr.orloca.norm: no visible binding for global variable
  ‘buttonsFrame’
Rcmdr.rloca.p: no visible binding for global variable ‘top’
Rcmdr.rloca.p: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsum: no visible binding for global variable ‘top’
Rcmdr.zsum: no visible binding for global variable ‘buttonsFrame’
Rcmdr.zsummin: no visible binding for global variable ‘top’
Rcmdr.zsummin : onOK: no visible binding for global variable
  ‘algorithmVariable’
Rcmdr.zsummin : onOK: no visible binding for global variable ‘.sol’
Rcmdr.zsummin: no visible binding for global variable ‘algorithmFrame’
Rcmdr.zsummin: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  .sol algorithmFrame algorithmVariable buttonsFrame normaFrame
  normaVariable top
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’ [99s/99s]
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 (0.15 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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Timing stopped at: 0.009 0.001 0.009
Error in spmat$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.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/RcppCWB.Rcheck/00install.out’ for details.
installed size is 31.1Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     22.9Mb
Running ‘doRUnit.R’ [86s/88s]
Running the tests in ‘tests/doRUnit.R’ failed.
Last 13 lines of output:
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector): ERROR !! 
  Error executing .setUp before test.gsl.vector : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.input.SEXP): ERROR !! 
  Error executing .setUp before test.gsl.vector.input.SEXP : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.view): ERROR !! 
  Error executing .setUp before test.gsl.vector.view : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  .setUp (before test.gsl.vector.wrappers): ERROR !! 
  Error executing .setUp before test.gsl.vector.wrappers : Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
    Error 1 occurred building shared library.
  Error: TEST HAD ERRORS!
  Execution halted
Errors in running code in vignettes:
when running code in ‘RcppGSL-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 ‘RcppGSL-unitTests.R’:
Error: unit test problems: 14 errors
Execution halted
Error in re-building vignettes:
  ...
/usr/local/clang4/bin/../include/c++/v1/algorithm:1932:1: note: candidate function template not viable: requires 5 arguments, but 4 were provided
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
1 error generated.
make: *** [gsl.o] Error 1
Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
  Error 1 occurred building shared library.
gsl.cpp:293:5: error: no matching function for call to 'transform'
    std::transform(vec.begin(), vec.end(), res.begin(), ::sqrt);
    ^~~~~~~~~~~~~~
/usr/local/clang4/bin/../include/c++/v1/algorithm:1922:1: note: candidate template ignored: couldn't infer template argument '_UnaryOperation'
transform(_InputIterator __first, _InputIterator __last, _OutputIterator __result, _UnaryOperation __op)
^
/usr/local/clang4/bin/../include/c++/v1/algorithm:1932:1: note: candidate function template not viable: requires 5 arguments, but 4 were provided
transform(_InputIterator1 __first1, _InputIterator1 __last1, _InputIterator2 __first2,
^
1 error generated.
make: *** [gsl.o] Error 1
Error in sourceCpp(file.path(pathRcppTests, "cpp/gsl.cpp")) : 
  Error 1 occurred building shared library.

Error: processing vignette 'RcppGSL-unitTests.Rnw' failed with diagnostics:
 chunk 2 (label = unitTesting) 
Error in eval(expr, .GlobalEnv) : unit test problems: 14 errors
Execution halted
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  9.3Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
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.
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.
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  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Running examples in ‘Rdimtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: do.rsir
> ### Title: Regularized Sliced Inverse Regression
> ### Aliases: do.rsir
> 
> ### ** Examples
> 
> ## generate swiss roll with auxiliary dimensions
> ## it follows reference example from LSIR paper.
> n = 123
> theta = runif(n)
> h     = runif(n)
> t     = (1+2*theta)*(3*pi/2)
> X     = array(0,c(n,10))
> X[,1] = t*cos(t)
> X[,2] = 21*h
> X[,3] = t*sin(t)
> X[,4:10] = matrix(runif(7*n), nrow=n)
> 
> ## corresponding response vector
> y = sin(5*pi*theta)+(runif(n)*sqrt(0.1))
> 
> ## try with different regularization methods
> ## use default number of slices
> out1 = do.rsir(X, y, regmethod="Ridge")
> out2 = do.rsir(X, y, regmethod="Tikhonov")
> out3 = do.rsir(X, y, regmethod="PCA")
> out4 = do.rsir(X, y, regmethod="PCARidge")
Warning in eigs_real_gen(A, nrow(A), k, which, sigma, opts, mattype = "matrix") :
  only 1 eigenvalue(s) converged, less than k = 2
> out5 = do.rsir(X, y, regmethod="PCATikhonov")
> outsir = do.sir(X, y)
> 
> ## visualize
> par(mfrow=c(2,3))
> plot(out1$Y[,1], out1$Y[,2], main="RSIR::Ridge")
> plot(out2$Y[,1], out2$Y[,2], main="RSIR::Tikhonov")
> plot(out3$Y[,1], out3$Y[,2], main="RSIR::PCA")
> plot(out4$Y[,1], out4$Y[,2], main="RSIR::PCA+Ridge")
Error in out4$Y[, 2] : subscript out of bounds
Calls: plot -> plot.default -> xy.coords
Execution halted
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]="./webshot579925e0d894.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot579925e0d894.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
Packages suggested but not available for checking: ‘interval’ ‘Icens’
Package unavailable to check Rd xrefs: ‘interval’
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 25.5Mb
  sub-directories of 1Mb or more:
    libs  24.7Mb
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/RtmpmzP1CJ/mbundle8ad954e716ea.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.
Package unavailable to check Rd xrefs: ‘installr’
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
Tbsb : ksiint: no visible global function definition for ‘pgamma’
Tbsb: no visible global function definition for ‘pchisq’
Tbsc: no visible global function definition for ‘qchisq’
riv_classical: no visible global function definition for ‘cov’
riv_classical: no visible global function definition for ‘pt’
riv_sest: no visible global function definition for ‘pt’
riv_sest: no visible global function definition for ‘mad’
riv_sest: no visible global function definition for ‘mahalanobis’
riv_withDummies: no visible global function definition for ‘coef’
riv_withDummies : <anonymous>: no visible global function definition
  for ‘coef’
Undefined global functions or variables:
  coef cov mad mahalanobis pchisq pgamma pt qchisq
Consider adding
  importFrom("stats", "coef", "cov", "mad", "mahalanobis", "pchisq",
             "pgamma", "pt", "qchisq")
to your NAMESPACE file.
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  8.6Mb
  sub-directories of 1Mb or more:
    datasets   8.6Mb
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’
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  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
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
Packages suggested but not available for checking: ‘topGO’ ‘DESeq’
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
Package suggested but not available for checking: ‘RnavGraph’
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
Packages suggested but not available for checking: ‘rrdf’ ‘Sxslt’
installed size is 93.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     91.1Mb
installed size is 17.9Mb
  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
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.
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.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'rpms_2017_02_10.tex' failed.
LaTeX errors:
! LaTeX Error: File `tikz-qtree.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
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.
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 14.3Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
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 43.4Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  42.0Mb
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
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Error in re-building vignettes:
  ...

Attaching package: ‘rstpm2’

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

    colon

Warning in log(-log(as.vector(S))) : NaNs produced
Warning in log(-log(as.vector(S))) : NaNs produced
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Introduction.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.10 \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/Rsymphony.Rcheck/00install.out’ for details.
.forest.plot: no visible global function definition for ‘par’
.forest.plot: no visible global function definition for ‘plot’
.forest.plot: no visible global function definition for ‘abline’
.forest.plot: no visible global function definition for ‘arrows’
.forest.plot: no visible global function definition for ‘points’
.forest.plot.scale: no visible global function definition for ‘par’
.forest.plot.scale: no visible global function definition for ‘plot’
.forest.plot.scale: no visible global function definition for ‘axTicks’
.forest.plot.scale : <anonymous>: no visible global function definition
  for ‘lines’
.forest.plot.scale: no visible global function definition for ‘lines’
.forest.plot.scale: no visible global function definition for ‘text’
.rtf.plot: no visible global function definition for ‘png’
.rtf.plot: no visible global function definition for ‘dev.off’
.rtf.trellis.object: no visible global function definition for ‘png’
.rtf.trellis.object: no visible global function definition for
  ‘dev.off’
addSessionInfo.RTF: no visible global function definition for
  ‘sessionInfo’
Undefined global functions or variables:
  abline arrows axTicks dev.off lines par plot png points sessionInfo
  text
Consider adding
  importFrom("grDevices", "dev.off", "png")
  importFrom("graphics", "abline", "arrows", "axTicks", "lines", "par",
             "plot", "points", "text")
  importFrom("utils", "sessionInfo")
to your NAMESPACE file.
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 45.4Mb
  sub-directories of 1Mb or more:
    libs  44.7Mb
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
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
Namespace in Imports field not imported from: ‘lexicon’
  All declared Imports should be used.
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
Package suggested but not available for checking: ‘MAST’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
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
Namespaces in Imports field not imported from:
  ‘DT’ ‘data.table’ ‘gridExtra’ ‘knitr’ ‘latticeExtra’ ‘msm’ ‘plotly’
  ‘xtable’
  All declared Imports should be used.
Packages required and available but unsuitable versions: ‘httpuv’ ‘later’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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
Package suggested but not available for checking: ‘edgeR’
Errors in running code in vignettes:
when running code in ‘SIBER.Rnw’
  ...

> SIBER(y = log(Dat[1, ] + 1), model = "NL")
      mu1       mu2    sigma1    sigma2       pi1     delta        BI 
6.2297063 6.8917722 0.3672838 0.3672838 0.1016360 1.8026005 0.5446901 

> library(edgeR)

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

Error: processing vignette 'SIBER.Rnw' failed with diagnostics:
 chunk 8 
Error in library(edgeR) : there is no package called ‘edgeR’
Execution halted
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
Package unavailable to check Rd xrefs: ‘copula’
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’
Namespace in Imports field not imported from: ‘ISLR’
  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 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  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   6.1Mb
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’ ‘ALL’
  ‘org.Hs.eg.db’
Packages unavailable to check Rd xrefs: ‘ALL’, ‘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, 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]="./webshot6a7810b92a16.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6a7810b92a16.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.
bbox_to_SpatialPolygons: no visible global function definition for
  ‘CRS’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygon’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘Polygons’
bbox_to_SpatialPolygons: no visible global function definition for
  ‘SpatialPolygons’
list.raster.files: no visible global function definition for ‘CRS’
list.raster.files: no visible global function definition for
  ‘spTransform’
list.raster.files: no visible global function definition for
  ‘SpatialPolygonsDataFrame’
list.raster.files: no visible global function definition for ‘spChFIDs’
predict_rasterEngine : predict.rasterEngine_function: no visible global
  function definition for ‘complete.cases’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘spTransform’
projectRaster_rigorous : chunk_function: no visible global function
  definition for ‘CRS’
spatial_sync_raster: no visible global function definition for ‘bbox’
spatial_sync_vector: no visible global function definition for
  ‘spTransform’
spatial_sync_vector: no visible global function definition for ‘CRS’
Undefined global functions or variables:
  CRS Polygon Polygons SpatialPolygons SpatialPolygonsDataFrame bbox
  complete.cases spChFIDs spTransform
Consider adding
  importFrom("stats", "complete.cases")
to your NAMESPACE file.
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
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
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.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
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  6.9Mb
  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
.jgrRun: no visible global function definition for ‘capture.output’
.macDlgList: no visible global function definition for ‘select.list’
.unixDlgForm: no visible global function definition for ‘as’
.unixDlgMessage: no visible global function definition for ‘alarm’
.winDlgList: no visible global function definition for ‘select.list’
dlgForm.textCLI: no visible global function definition for ‘as’
dlgList.textCLI: no visible global function definition for
  ‘select.list’
dlgMessage.textCLI: no visible global function definition for
  ‘select.list’
dlgSave.textCLI: no visible global function definition for
  ‘select.list’
Undefined global functions or variables:
  alarm as capture.output select.list
Consider adding
  importFrom("methods", "as")
  importFrom("utils", "alarm", "capture.output", "select.list")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
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.
Namespaces in Imports field not imported from:
  ‘rgeos’ ‘stringr’
  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/sybilSBML.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘sylly.de’ ‘sylly.en’ ‘sylly.es’
Package suggested but not available for checking: ‘mpoly’
Running examples in ‘symmoments-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert.mpoly
> ### Title: Convert between mpoly and list representations of multivariate
> ###   polynomials
> ### Aliases: ' convert.mpoly '
> 
> ### ** Examples
> 
> # create an mpoly object here
> 
> # convert from mpoly to list representation
> library(mpoly)
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Errors in running code in vignettes:
when running code in ‘symmoments.rnw’
  ...
[4,]    1    1    1    2

> evaluate(m1234, c(4, 2, 1, 1, 3, 1, 1, 2, 1, 2))
[1] 3480

> library(mpoly)

  When sourcing ‘symmoments.R’:
Error: there is no package called ‘mpoly’
Execution halted
Error in re-building vignettes:
  ...
Loading required package: mvtnorm
Loading required package: cubature
Loading required package: combinat

Attaching package: ‘combinat’

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

    combn

Loading required package: multipol
Loading required package: abind

Attaching package: ‘multipol’

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

    single


Error: processing vignette 'symmoments.rnw' failed with diagnostics:
 chunk 13 (label = noncentral3a) 
Error in library(mpoly) : there is no package called ‘mpoly’
Execution halted
Namespaces with empty importFrom:
  ‘Rcpp’ ‘methods’
Packages suggested but not available for checking: ‘tigris’ ‘rgdal’
Namespaces in Imports field not imported from:
  ‘knitr’ ‘lazyeval’ ‘rlang’
  All declared Imports should be used.
Packages suggested but not available for checking: ‘GISTools’ ‘rgeos’
Running examples in ‘tbart-Ex.R’ failed
The error most likely occurred in:

> ### Name: allocate
> ### Title: Teitz-Bart algorithm applied to Spatial* and Spatial*DataFrame
> ###   objects
> ### Aliases: allocate
> 
> ### ** Examples
> 
> data(meuse)
> coordinates(meuse) <- ~x+y
> allocate(meuse,p=5)
  [1]   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9   9  23
 [19]  23  23  23  23  23   9   9   9  23  23  23   9  23  23  23  23  23  23
 [37]  23  23  23  23  23 132 132 132 132 132 132 132 132 132 132 132 132 132
 [55] 132 132 132 132 132 132 132 113 113 113 113 113 113 113 113  77  77  77
 [73]  77  77  77  77  77  77  77  77  77 113 113   9 113 113  77  77  77  77
 [91]  77  77  77  77  77  77  77  77  77  77  77 113 113 113 113 132 113 113
[109] 113 113 113 113 113 113 113 113 113 113 132 132 132 132 132 132 132 132
[127] 132 132   9  23 113 132  23 132 113 113 113  77  77  77  77  77  77  77
[145]  77  77  77  77  77  77  77  77  77  77 113
> 
> 
> 
> require(RColorBrewer)
Loading required package: RColorBrewer
> require(GISTools)
Loading required package: GISTools
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘GISTools’
> data(georgia)
Warning in data(georgia) : data set ‘georgia’ not found
> allocations.list <- allocate(georgia2,p=5)
Error in allocate(georgia2, p = 5) : object 'georgia2' not found
Execution halted
Packages suggested but not available for checking: ‘edgeR’ ‘DESeq2’
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    sql   8.7Mb
Errors in running code in vignettes:
when running code in ‘tcpl_Overview.Rnw’
  ...
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
Assertion failure at kmp_runtime.cpp(6480): __kmp_thread_pool == __null.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.
OMP: Error #13: Assertion failure at kmp_runtime.cpp(6480).
OMP: Hint: Please submit a bug report with this message, compile and run commands used, and machine configuration info including native compiler and operating system versions. Faster response will be obtained by including all program sources. For information on submitting this issue, please see http://www.intel.com/software/products/support/.

  When sourcing ‘tcpl_Overview.R’:
Error: argument to 'which' is not logical
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  34.3Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tdthap-paper.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
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs       7.2Mb
    tessdata  31.0Mb
Packages in Depends field not imported from:
  ‘boot’ ‘survrec’
  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:
    libs   4.7Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/textTinyR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: textutils

Attaching package: 'textutils'

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

    toHTML

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'btable.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
Error in re-building vignettes:
  ...
Loading required package: Tides
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(dry$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(wet$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Warning in gapsts(wet$time, dtMax, unit = unit, shiftbegin = TRUE) :
  First data point is beginning of gap. To shift t0, dt is estimated from next continuous series
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Tides.tex' failed.
BibTeX errors:
The top-level auxiliary file: Tides.aux
I couldn't open style file apalike2.bst
---line 14 of file Tides.aux
 : \bibstyle{apalike2
 :                   }
I'm skipping whatever remains of this command
I found no style file---while reading file Tides.aux
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 111-113 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
.viterbiTrainingEmission,contHMM-list-list: no visible global function
  definition for ‘var’
sampleObs,tDist-numeric: no visible global function definition for ‘rt’
Undefined global functions or variables:
  rt var
Consider adding
  importFrom("stats", "rt", "var")
to your NAMESPACE file.
Errors in running code in vignettes:
when running code in ‘tileHMM.Rnw’
  ...

> h3k27.data <- as.matrix(simChIP[, 7:14])

> h3k27.data <- log(h3k27.data, 2)

> h3k27.norm <- preprocessCore::normalize.quantiles(h3k27.data)

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

Error: processing vignette 'tileHMM.Rnw' failed with diagnostics:
 chunk 3 
Error in loadNamespace(name) : 
  there is no package called ‘preprocessCore’
Execution halted
'library' or 'require' call to ‘ggplot2’ 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: ‘microbenchmark’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
determine_replications: no visible global function definition for
  ‘microbenchmark’
do_timeit: no visible global function definition for ‘Rprof’
do_timeit: no visible global function definition for ‘summaryRprof’
mean.timeit: no visible global function definition for ‘aggregate’
plot.timeit: no visible global function definition for ‘ggplot’
plot.timeit: no visible global function definition for ‘aes’
plot.timeit: no visible global function definition for ‘geom_boxplot’
plot.timeit: no visible global function definition for ‘geom_point’
plot.timeit: no visible global function definition for ‘xlab’
plot.timeit: no visible global function definition for ‘ylab’
plot.timeit: no visible global function definition for ‘ggtitle’
plot.timeit: no visible global function definition for ‘coord_flip’
timeit: no visible binding for global variable ‘median’
Undefined global functions or variables:
  Rprof aes aggregate coord_flip geom_boxplot geom_point ggplot ggtitle
  median microbenchmark summaryRprof xlab ylab
Consider adding
  importFrom("stats", "aggregate", "median")
  importFrom("utils", "Rprof", "summaryRprof")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘rgl’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
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
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'tmle-npvi.tex' failed.
LaTeX errors:
! LaTeX Error: File `manfnt.sty' not found.

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

! Emergency stop.
<read *> 
         
l.59 \usepackage
                [textwidth=15cm, textheight=23cm]{geometry}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
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 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 'Expanding_TR8.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.10 \usepackage
                {graphicx}^^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 'traitr.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.15 \usepackage
                {amsmath}            % for amslatex stuff^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Namespaces in Imports field not imported from:
  ‘ggplot2’ ‘magrittr’ ‘rgeos’
  All declared Imports should be used.
Packages suggested but not available for checking:
  ‘rgdal’ ‘rgeos’ ‘OpenStreetMap’
Package unavailable to check Rd xrefs: ‘rgeos’
Running ‘tracks.R’ [2s/3s]
Running the tests in ‘tests/tracks.R’ failed.
Complete output:
  > Sys.setenv(TZ = "Europe/Berlin")
  > # Load required libraries.
  > 
  > library(sp)
  > library(spacetime)
  > library(trajectories)
  > library(rgdal)
  Error in library(rgdal) : there is no package called 'rgdal'
  Execution halted
Error in re-building vignettes:
  ...
Warning in add.known.TRAMPknowns(x$knowns, x$samples, sample.fk, ...) :
  Mutiple peaks per enzyme/primer combination for sample 221, taking largest peaks only
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TRAMPRdemo.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
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 `wrapfig.sty' not found.

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

! Emergency stop.
<read *> 
         
l.10 \usepackage
                {rotating}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: trapezoid
Loading required package: plyr
Loading required package: ggplot2
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'trapezoid.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.13 \usepackage
                {graphicx}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘treeHFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawViterbiTree
> ### Title: Arranges a Viterbi tree
> ### Aliases: DrawViterbiTree
> ### Keywords: misc
> 
> ### ** Examples
> 
> ## Fit a continous treeHFM ## 
> nHStates = 2;
> ########create observation sequences########
> obs1 <- rbind(runif(10,0,1),runif(10,0,1))
> obs2 <- rbind(runif(8,0,1),runif(8,0,1))
> data=list()
> data[[1]]=obs1
> data[[2]]=obs2
> ######### create guesses for gaussian covariance matrix and means #########
> mc2 <- Mclust(t(cbind(obs1,obs2)), G=2)
> muInit=mc2$parameters$mean;
> SigmaInit=mc2$parameters$variance$sigma
> #########create tree topology####################################
> nodeIndices1=cbind(c(0,1,2,3,3,4,5,6,7,8),c(1,2,3,4,5,6,7,8,9,10));
> nodeIndices2=cbind(c(0,1,2,3,4,4,5,6),c(1,2,3,4,5,6,7,8));
> dataNodeIndices=list()
> dataNodeIndices[[1]]=nodeIndices1;
> dataNodeIndices[[2]]=nodeIndices2;
> ######### create guesses for prior and transition matrices#########
> prior1=array(1,nHStates);
> priorInit = array(1,nHStates)/nHStates;
> transmatInit = matrix(1,nHStates,nHStates)*(1/nHStates);
> transInitDiv= matrix(1,nHStates,nHStates*nHStates)*(1/(nHStates*nHStates))
> #
> hfm=HFMfit(data,nHStates,dataNodeIndices,priorInit,transmatInit,transInitDiv,'c',
+ SigmaInit=SigmaInit, muInit=muInit);

 *** caught segfault ***
address 0x8, cause 'memory not mapped'

Traceback:
 1: .Call("RWrapperBM", priorInit, transmatInit, transInitDiv, emissionProb,     data, nodeIndices, parents, summationIndices, indicesXD,     type, stateIndicesSingle, nHStates, nDStates, nObs, dimData,     nEStates, SigmaInit, muInit)
 2: HFMfit(data, nHStates, dataNodeIndices, priorInit, transmatInit,     transInitDiv, "c", SigmaInit = SigmaInit, muInit = muInit)
An irrecoverable exception occurred. R is aborting now ...
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
negative edges length changed to 0!
Quitting from lines 115-133 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.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 139-141 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-71 (trip.Rmd) 
Error: processing vignette 'trip.Rmd' failed with diagnostics:
there is no package called 'rgdal'
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'qexpfamily.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.35 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  ./tsBSS.h:10:22: warning: 'varExx_k' has C-linkage specified, but returns user-defined type 'arma::mat' (aka 'Mat<double>') which is incompatible with C [-Wreturn-type-c-linkage]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/tsBSS.Rcheck/00install.out’ for details.
Packages which this enhances but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’
Packages suggested but not available for checking:
  ‘TSPostgreSQL’ ‘TSodbc’ ‘RPostgreSQL’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSPostgreSQL’, ‘TSodbc’, ‘RPostgreSQL’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]
Apr 02, 2017 10:18:16 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient getData
INFO: The sdmx call returned messages in the footer:
 Message [code=400, severity=Error, url=null, text=[Error caused by the caller due to incorrect or semantically invalid arguments]]

  When sourcing ‘Guide.R’:
Error: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxXmlContentException: The query: ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT did not match any time series on the provider.
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
Package unavailable to check Rd xrefs: ‘TSPostgreSQL’
Error in re-building vignettes:
  ...
Error: processing vignette 'tsdisagg2manual.ltx' failed with diagnostics:
Running 'texi2dvi' on 'tsdisagg2manual.ltx' 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.16 \usepackage
                {enumerate}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Execution halted
Error in re-building vignettes:
  ...
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).
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]="./webshot43b24adea0a5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot43b24adea0a5.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
Running examples in ‘tuneRanger-Ex.R’ failed
The error most likely occurred in:

> ### Name: estimateTimeTuneRanger
> ### Title: estimateTimeTuneRanger
> ### Aliases: estimateTimeTuneRanger
> 
> ### ** Examples
> 
> estimateTimeTuneRanger(iris.task)
Error in setHyperPars2.Learner(learner, insert(par.vals, args)) : 
  order is not feasible for parameter 'respect.unordered.factors'!
Calls: estimateTimeTuneRanger ... setHyperPars -> setHyperPars2 -> setHyperPars2.Learner
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 1. Error: classification ranger (@test_base.R#15)  ──────────────────────────
  order is not feasible for parameter 'respect.unordered.factors'!
  1: estimateTimeTuneRanger(iris.task, num.trees = 100, num.threads = 1) at testthat/test_base.R:15
  2: makeLearner(paste0(type, ".ranger"), par.vals = par.vals, predict.type = predict.type)
  3: setHyperPars(learner = wl, ..., par.vals = par.vals)
  4: setHyperPars2(learner, insert(par.vals, args))
  5: setHyperPars2.Learner(learner, insert(par.vals, args))
  6: stop(msg)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: classification ranger (@test_base.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
accelerate: no visible global function definition for ‘modifyList’
boxplot.turbosim: no visible global function definition for ‘par’
boxplot.turbosim: no visible global function definition for ‘axis’
boxplot.turbosim: no visible global function definition for ‘mtext’
dataprof.turbosim: no visible global function definition for ‘quantile’
dataprof.turbosim: no visible global function definition for ‘par’
dataprof.turbosim: no visible global function definition for ‘plot’
dataprof.turbosim: no visible global function definition for ‘lines’
dataprof.turbosim: no visible global function definition for ‘segments’
dataprof.turbosim: no visible global function definition for ‘legend’
line.search: no visible global function definition for ‘optimize’
pairs.turbosim: no visible global function definition for ‘par’
pairs.turbosim: no visible global function definition for ‘plot’
pairs.turbosim: no visible global function definition for ‘legend’
pairs.turbosim: no visible global function definition for ‘axis’
pairs.turbosim: no visible global function definition for ‘title’
pairs.turbosim: no visible global function definition for ‘coef’
pairs.turbosim: no visible global function definition for ‘abline’
pairs.turbosim: no visible global function definition for ‘text’
plot.turbo: no visible global function definition for ‘plot’
plot.turbo: no visible global function definition for ‘lines’
plot.turbo: no visible global function definition for ‘legend’
turboSim: no visible binding for global variable ‘par’
turboem: no visible global function definition for ‘modifyList’
Undefined global functions or variables:
  abline axis coef legend lines modifyList mtext optimize par plot
  quantile segments text title
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "lines", "mtext",
             "par", "plot", "segments", "text", "title")
  importFrom("stats", "coef", "optimize", "quantile")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Attaching package: ‘survey’

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

    dotchart

Loading required package: xtable
Loading required package: latticeExtra
Loading required package: RColorBrewer
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'iptw.tex' failed.
LaTeX errors:
! LaTeX Error: File `srcltx.sty' not found.

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

! Emergency stop.
<read *> 
         
l.11 \usepackage
                {url}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    doc         5.3Mb
    dummydata   1.4Mb
    libs       21.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Umpire.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.15 \pagestyle
               {myheadings}^^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 'design.tex' failed.
LaTeX errors:
! LaTeX Error: File `apalike.sty' not found.

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

! Emergency stop.
<read *> 
         
l.6 \usepackage
               {amsmath}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: residuals.MxModel
> ### Title: Get residuals from an MxModel
> ### Aliases: residuals.MxModel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> latents  = c("g")
> manifests = names(demoOneFactor)
> 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)
+ )
> m1 = umxRun(m1, setLabels = TRUE, setValues = TRUE)
Running One Factor with 10 parameters
Error in runHelper(model, frontendStart, intervals, silent, suppressWarnings,  : 
  c++ exception (unknown reason)
Calls: umxRun -> mxRun -> runHelper
Execution halted
Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: message(e)
  7: withRestarts({
         signalCondition(cond)
         defaultHandler(cond)
     }, muffleMessage = function() NULL)
  8: withOneRestart(expr, restarts[[1L]])
  9: doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 54 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_umx_has_CI.r#41) 
  2. Error: (unknown) (@test_umx_is_RAM.r#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: reshape
Loading required package: lattice
Loading required package: parallel
Loading required package: Rcpp
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cap-recap.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 \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.
Quitting from lines 126-127 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
lexical error: invalid char in json text.
                                	      <!DOCTYPE html PUBLIC "-//W3C//
                     (right here) ------^
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
Warning: 'data' shows efficiency > 1; this looks almost too good to be true
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'usl.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.65 \usepackage
                [scaled=0.85]{beramono}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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 the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.1Mb
'library' or 'require' call to ‘foreach’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘foreach’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
constant.post.9mo: no visible global function definition for ‘pexp’
ll.coverage.optim.const.post.9m: no visible global function definition
  for ‘dexp’
make.sample.pop: no visible global function definition for ‘runif’
mcmc.converge: no visible global function definition for ‘par’
mcmc.converge: no visible global function definition for ‘plot’
mcmc.converge: no visible global function definition for ‘points’
mcmc.converge: no visible global function definition for ‘density’
mcmc.converge: no visible global function definition for ‘lines’
mcmc.converge : <anonymous>: no visible global function definition for
  ‘sd’
mcmc.estimate : run.chain: no visible global function definition for
  ‘dexp’
mcmc.estimate : run.chain: no visible global function definition for
  ‘rnorm’
mcmc.estimate : run.chain: no visible global function definition for
  ‘runif’
mcmc.estimate : run.chain: no visible global function definition for
  ‘par’
mcmc.estimate : run.chain: no visible global function definition for
  ‘plot’
mcmc.estimate: no visible global function definition for ‘%dopar%’
mcmc.estimate: no visible global function definition for ‘foreach’
sim.n.vacc.sample.pop : <anonymous>: no visible global function
  definition for ‘runif’
vaccinate.sample.pop: no visible global function definition for ‘runif’
Undefined global functions or variables:
  %dopar% density dexp foreach lines par pexp plot points rnorm runif
  sd
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("stats", "density", "dexp", "pexp", "rnorm", "runif", "sd")
to your NAMESPACE file.
Running ‘coverageTest.r’ [0s/1s]
Running the tests in ‘tests/coverageTest.r’ failed.
Last 13 lines of output:
  > #*  
  > #*  $Id: coverageTest.r 378 2012-01-27 02:35:09Z ken $
  > #*  ----------------------------------------------------------------------------
  > 
  > 
  > # TBD: Add file header
  > # TBD: Do I need some 'library( pkg )' or 'source( file )' calls here???
  > 
  > 
  > # source( "../tests/testUtils.r" )
  > source( getTestPaths("vacem","tests/testUtils.r") )
  Error in getTestPaths("vacem", "tests/testUtils.r") : 
    could not find function "getTestPaths"
  Calls: source
  Execution halted
Packages suggested but not available for checking:
  ‘vaers’ ‘vaersND’ ‘devtools’
Missing or unexported object: ‘validate::%vin%’
Package suggested but not available for checking: ‘GenomicRanges’
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/VBmix.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
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 has_utility("pdfcrop") :
  pdfcrop not installed or not in PATH
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vdg.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.75 \usepackage
                {algorithmic}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Loading required package: vegan
Loading required package: permute
Loading required package: lattice
This is vegan 2.4-4
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'MedRegExample.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
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  26.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.7Mb
Error in re-building vignettes:
  ...

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

    backsolve

Loading required package: grid
Warning in structure(ia, dimnames = NULL) :
  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 'ConfoundingPotential.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.25 \usepackage
                {keyval}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
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 the system RNG.

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 51.6Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  49.2Mb
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 'walkr.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/wand.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘pbmcapply’ ‘proxy’ ‘signal’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
There are  2000 missing values for 05054000 or 49.78 percent of the data.
The maximum block of missing 05054000 data is 12 days long.
Filled in 2000 values for 05054000
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
Error in re-building vignettes:
  ...
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Watersheds.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.14 \bibliographystyle
                       {apacite}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

trying URL 'http://www.webgestalt.org/data/goslim/hsapiens_GOSlim_MolecularFunction.table'
Content type 'unknown' length 1122875 bytes (1.1 MB)
==================================================
downloaded 1.1 MB

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WebGestaltR.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
Namespace in Imports field not imported from: ‘fauxpas’
  All declared Imports should be used.
Package suggested but not available for checking: ‘rgeolocate’
Error in re-building vignettes:
  ...
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
 [>] 490 sequences with 6 distinct states
 [>] creating a 'sm' with a single substitution cost of 1
 [>] creating 6x6 substitution-cost matrix using 1 as constant value
 [>] 490 distinct sequences
 [>] min/max sequence length: 70/70
 [>] computing distances using the HAM metric
 [>] elapsed time: 0.17 secs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WeightedClusterPreview.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.78 \usepackage
                {afterpage}^^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 'Definition.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
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'funwithfunload.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
Package suggested but not available for checking: ‘genefilter’
Unexported objects imported by ':::' calls:
  ‘circular:::DensityCircularRad’ ‘circular:::DvonmisesRad’
  ‘circular:::DwrappednormalRad’ ‘circular:::MlevonmisesRad’
  ‘circular:::MlewrappednormalRad’
  See the note in ?`:::` about the use of this operator.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'wrappedvig.ltx' failed with diagnostics:
Running 'texi2dvi' on 'wrappedvig.ltx' failed.
LaTeX errors:
! Package pdftex.def Error: File `wrappedv1-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 `wrappedv2-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 `wrappedv3-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 `wrappedv4-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                
Execution halted
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/soccer2-plot1-1-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 `figure/goggles-plot1-1-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 `figure/swim-plot1-1-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 `figure/swim2-plot1-1-eps-converted-to.pdf' no
t found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘GenomicScores’ ‘ggbio’
Error in re-building vignettes:
  ...
Loading required package: Xmisc

Attaching package: ‘Xmisc’

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

    dir.exists

Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Xmisc-ArgumentParser.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
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
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 'OtherPackagesGallery.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.67 \usepackage
                {hyperref} % hyperref last^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘MBESS’
Running examples in ‘yhat-Ex.R’ failed
The error most likely occurred in:

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Package suggested but not available for checking: ‘loon’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'zipfr-tutorial.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.13 \setpapersize
                  [portrait]{A4}^^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/zstdr.Rcheck/00install.out’ for details.
ztable.glm: no visible global function definition for ‘confint’
ztable.glm: no visible global function definition for ‘coef’
ztable.nls: no visible global function definition for ‘formula’
Undefined global functions or variables:
  coef confint formula
Consider adding
  importFrom("stats", "coef", "confint", "formula")
to your NAMESPACE file.