Error in re-building vignettes:
  ...

Attaching package: 'scales'

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

    discard


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'GGally'

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

    nasa

Quitting from lines 337-354 (exploring-election-data.Rmd) 
Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics:
could not find function "dmap"
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Error in re-building vignettes:
  ...
ggtree v1.6.11  For help: https://guangchuangyu.github.io/ggtree

If you use ggtree in published research, please cite:
Guangchuang Yu, David Smith, Huachen Zhu, Yi Guan, Tommy Tsan-Yuk Lam. ggtree: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods in Ecology and Evolution 2017, 8(1):28-36, doi:10.1111/2041-210X.12628
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
argument is not interpretable as logical
Execution halted
Missing or unexported object: 'xcms::profMat'
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running 'testthat.R' [113s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Predictor:	 Target 
  Formula:	 Prop ~ Target 
  Runs of Significant Time Bins: 
  Positive Run 1  ===== 
  	Time:		 15900 - 21000 -- 1. Error: (unknown) (@test_cluster_analysis.R#143)  -------------------------
  no applicable method for 'make_time_cluster_data' applied to an object of class "data.frame"
  1: make_time_cluster_data(response_time_by_ppt, predictor_column = "Sex", test = "boot_splines", 
         within_subj = FALSE, smoother = "smooth.spline", alpha = 0.05) at testthat/test_cluster_analysis.R:143
  
  == testthat results  ===========================================================
  OK: 42 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_cluster_analysis.R#143) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: RSQLite
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
path for html_dependency not found: 
Execution halted
Package required but not available: 'CVXR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'fpctests.R' [15s]
Running the tests in 'tests/fpctests.R' failed.
Last 13 lines of output:
  [10,]    1
  > 
  > set.seed(20000)
  > x1 <- rnorm(50)
  > y <- rnorm(100)
  > x2 <- rnorm(40,mean=20)
  > x3 <- rnorm(10,mean=25,sd=100)
  > x0 <- cbind(c(x1,x2,x3),y)
  > 
  > prediction.strength(x0,M=10,Gmax=4,
  +                            clustermethod=noisemclustCBI,
  +                            classification="qda")
  Error in `[.default`(ctable, kk, ) : subscript out of bounds
  Calls: prediction.strength -> [ -> [.table -> NextMethod
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.7Mb
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 59-70 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics:
replacement has 0 rows, data has 54
Execution halted
Package required but not available: 'gge'

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

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

> ### Name: gglagplot
> ### Title: Plot time series against lagged versions of themselves
> ### Aliases: gglagplot
> 
> ### ** Examples
> 
> gglagplot(AirPassengers)
Error: `x` must be a vector, not a ts object, do you want `stats::lag()`?
Execution halted
Running 'test-all.R' [76s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  8: eval_bare(dot$expr, dot$env)
  9: lapply(seq(1:lags), .lag)
  10: FUN(X[[i]], ...)
  11: as.vector(lag(ts, k))
  12: lag(ts, k)
  13: bad_args("x", "must be a vector, not a ts object, do you want `stats::lag()`?")
  14: glubort(fmt_args(args), ..., .envir = .envir)
  15: .abort(text)
  
  == testthat results  ===========================================================
  OK: 1442 SKIPPED: 9 FAILED: 1
  1. Error: gglagplot (@test-tslib.R#103) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'grid'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 34 SKIPPED: 0 FAILED: 12
  1. Error: Install: ask no (@test-gh_install_packages.R#27) 
  2. Error: Install: ask yes (@test-gh_install_packages.R#37) 
  3. Error: recommend_dependencies: ask = TRUE (@test-utils_for_install.R#49) 
  4. Error: select_repository: multi candidates (@test-utils_for_install.R#130) 
  5. Error: select_repository: cancel (@test-utils_for_install.R#142) 
  6. Error: remove_conflict_repos: no installed (@test-utils_for_install.R#169) 
  7. Error: remove_conflict_repos: not conflict (@test-utils_for_install.R#183) 
  8. Error: remove_conflict_repos: conflict GitHub, ask yes (@test-utils_for_install.R#198) 
  9. Error: remove_conflict_repos: conflict GitHub, ask no (@test-utils_for_install.R#213) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Running 'testthat.R' [55s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  4: FUN(X[[i]], ...)
  5: eval(subexpr_mod, envir = data_subexpr)
  6: eval(expr, envir, enclos)
  7: `-fr`(`[fr`(ability, player1), `[fr`(ability, player2))
  8: is_modfr(modfr1)
  9: `[fr`(ability, player1)
  
  == testthat results  ===========================================================
  OK: 69 SKIPPED: 2 FAILED: 3
  1. Error: prev_fit doesn't affect the result (@test_fit.R#125) 
  2. Error: (unknown) (@test_model_frames.R#20) 
  3. Error: (unknown) (@test_subformula.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [61s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  4: FUN(X[[i]], ...)
  5: eval(subexpr_mod, envir = data_subexpr)
  6: eval(expr, envir, enclos)
  7: `-fr`(`[fr`(ability, player1), `[fr`(ability, player2))
  8: is_modfr(modfr1)
  9: `[fr`(ability, player1)
  
  == testthat results  ===========================================================
  OK: 69 SKIPPED: 2 FAILED: 3
  1. Error: prev_fit doesn't affect the result (@test_fit.R#125) 
  2. Error: (unknown) (@test_model_frames.R#20) 
  3. Error: (unknown) (@test_subformula.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/gmum.r.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Neal Richardson <neal.p.richardson@gmail.com> [rev] (Neal reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
  Julia Gustavsen <j.gustavsen@gmail.com> [rev] (Julia reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-33\unhbox\voidb@x \penalty \@M \ {}1.
3/share/texmf/tex/latex/Sweave.sty' not found.

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
Package required and available but unsuitable version: 'ggtree'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
Running 'testthat.R' [77s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 57 SKIPPED: 23 FAILED: 11
  1. Error: Beta diversity from a list of phyloseq objects (@test-BD_ordinations.R#2) 
  2. Error: Beta diversity from a list of phyloseq objects (parallel) (@test-BD_ordinations.R#9) 
  3. Error: phyloseq sim (@test-HTSSIP_sim.R#59) 
  4. Error: phyloseq sim w/ metadata (@test-HTSSIP_sim.R#75) 
  5. Error: phyloseq sample_data can be converted to dataframe (@test-Util.R#10) 
  6. Error: phyloseq tax_table can be converted to dataframe (@test-Util.R#18) 
  7. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#25) 
  8. Error: phyloseq-rep sample_data can be converted to dataframe (@test-Util.R#35) 
  9. Error: phyloseq otu_table can be converted to dataframe (@test-Util.R#48) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.2Mb
    libs   2.4Mb
Authors@R field gives persons with no valid roles:
  Andee Kaplan [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
  Carl Ganz [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpOyVryK\ex_data1756c79727b2e.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpOyVryK\ex_data1756c79727b2e.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/2016_policydokument_manual_nationella-lungcancerregistret.pdf'
Execution halted
Running examples in 'infer-Ex.R' failed
The error most likely occurred in:

> ### Name: hypothesize
> ### Title: Declare a null hypothesis
> ### Aliases: hypothesize
> 
> ### ** Examples
> 
> # One binary variable
>   mtcars %>%
+     dplyr::mutate(am = factor(am)) %>%
+     specify(response = am, success = "1") %>%
+     hypothesize(null = "point", p = 0.75) %>%
+     generate(reps = 100, type = "simulate") %>%
+     calculate(stat = "prop")
Error in .subset2(x, i, exact = exact) : invalid subscript type 'symbol'
Calls: %>% ... [[.tbl_df -> NextMethod -> [[.data.frame -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 92-105 (flights_examples.Rmd) 
Error: processing vignette 'flights_examples.Rmd' failed with diagnostics:
invalid subscript type 'symbol'
Execution halted
Package required and available but unsuitable version: 'libcoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'iotools/libs/i386/iotools.dll':
  Found non-API call to R: 'getConnection'
File 'iotools/libs/x64/iotools.dll':
  Found non-API call to R: 'getConnection'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Namespace with empty importFrom: 'miscTools'
Found the following significant warnings:
  Warning: S3 methods '.DollarNames.Message', '.DollarNames.Descriptor', '.DollarNames.EnumDescriptor', '.DollarNames.EnumValueDescriptor', '.DollarNames.FileDescriptor', '.DollarNames.FieldDescriptor', '.DollarNames.ServiceDescriptor', '.DollarNames.MethodDescriptor', '.DollarNames.ZeroCopyInputStream', '.DollarNames.ZeroCopyOutputStream', 'with.Message', 'within.Message', 'as.list.Message', 'as.list.Descriptor', 'as.list.EnumDescriptor', 'as.list.FileDescriptor', 'as.list.ServiceDescriptor' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.3/jmvcore.Rcheck/00install.out' for details.
StartKappa: no visible global function definition for 'read.csv'
StartKappa: no visible global function definition for 'na.omit'
StartKappa: no visible global function definition for 'write.csv2'
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/lazyWeave.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'partykit'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: (function (...) 
     .subset2(public_bind_env, "finalize")())(<environment>)
  10: .subset2(public_bind_env, "finalize")()
  11: is_open(self$con)
  12: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: The pipe function (@test_nse.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/markmyassignment.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 264-270 (estimaterates.Rmd) 
Error: processing vignette 'estimaterates.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.1     v dplyr   0.7.4
v tidyr   0.7.2     v stringr 1.2.0
v readr   1.1.1     v forcats 0.2.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Loading required package: lattice
Error in unloadNamespace(package) : 
  namespace 'lattice' is imported by 'nlme', 'Matrix', 'psych', 'mosaic' so cannot be unloaded
Error : .onAttach failed in attachNamespace() for 'mdsr', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package 'lattice' version 0.20.35 cannot be unloaded
Error: package or namespace load failed for 'mdsr'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error in re-building vignettes:
  ...
Setting options('download.file.method.GEOquery'='auto')
Setting options('GEOquery.inmemory.gpl'=FALSE)
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
path for html_dependency not found: 
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.6Mb
    misc   1.1Mb
Missing or unexported object: 'tools::CRAN_package_db'
Found the following significant warnings:
  Warning: replacing previous import 'BBmisc::isFALSE' by 'backports::isFALSE' when loading 'mlr'
See 'd:/Rcompile/CRANpkg/local/3.3/mlr.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'parallel'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/monoreg.Rcheck/00install.out' for details.
Running 'testthat.R' [8s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(mortAAR)
  > 
  > test_check("mortAAR")
  -- 1. Failure: prep.life.table imports a data set correct (@test_input_functions
  names(example_life_table) not equal to c("Unbestimmt", "Weiblich", "Männlich", "All").
  1/4 mismatches
  x[3]: "MÃ¤nnlich"
  y[3]: "Männlich"
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 1
  1. Failure: prep.life.table imports a data set correct (@test_input_functions.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
Note: significantly better compression could be obtained
        by using R CMD build --resave-data
           old_size new_size compress
  cgps.rda    1.5Mb    1.4Mb       xz
Authors@R field gives persons with no valid roles:
  YouGov [fnd]
Error in re-building vignettes:
  ...
pandoc.exe: Could not determine mime type for `https://raw.github.com/vincent-dk/msgl/master/fig1.png'
CallStack (from HasCallStack):
  error, called at src\Text\Pandoc\SelfContained.hs:156:35 in pandoc-1.19.2.1-3EiBhxep0x773HKxrkonLI:Text.Pandoc.SelfContained
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS README.utf8.md --to html --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output README.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.3\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 1
Error: processing vignette 'README.Rmd' failed with diagnostics:
pandoc document conversion failed with error 1
Execution halted
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             cat(msg)
         if (length(msg) == 0) {
             e = simpleError(paste(1:length(messages), messages, sep = ": ", collapse = ""))
             class(e) = c(class, class(e))
             stop(e)
         }
         messages <<- c(messages, msg)
     })(character(0))
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-NFP.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.2Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.2Mb
Error in re-building vignettes:
  ...
Warning: code chunks must not depend on the uncached chunk "raster-example"
Loading required package: sp
Warning: code chunks must not depend on the uncached chunk "raster-example2"
Loading required package: viridisLite
nlm_mpd returns RasterLayer with that fits in the dimension 2^n+1

     PLEASE NOTE:  The components "delsgs" and "summary" of the
 object returned by deldir() are now DATA FRAMES rather than
 matrices (as they were prior to release 0.0-18).
 See help("deldir").
 
     PLEASE NOTE: The process that deldir() uses for determining
 duplicated points has changed from that used in version
 0.0-9 of this package (and previously). See help("deldir").


Quitting from lines 42-186 (bestiary.Rmd) 
Error: processing vignette 'bestiary.Rmd' failed with diagnostics:
nrow(coords) > 0 is not TRUE
Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/npbr.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMPController.Rcheck/00install.out' for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    R        1.8Mb
    libs     5.8Mb
    models   4.8Mb
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required and available but unsuitable versions: 'libcoin' 'inum'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  8: all.equal(x, y, tolerance = tolerance, check.attributes = check.attributes, ...)
  9: all.equal.numeric(x, y, tolerance = tolerance, check.attributes = check.attributes, 
         ...)
  10: stop(gettextf("'%s' must be logical", "check.attributes"), domain = NA)
  
  == testthat results  ===========================================================
  OK: 78 SKIPPED: 0 FAILED: 5
  1. Error: when read_multipage standard type only (@test_multipage.R#79) 
  2. Error: when read_multipage journal-paper only (@test_multipage.R#90) 
  3. Error: when read_multipage journal-paper only (@test_multipage.R#97) 
  4. Error: when read_multipage journal-paper only (@test_multipage.R#104) 
  5. Error: expect_equal_scale is 10% tolerance (@test_utils.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   1.7Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[2]: "<chr>         "
  
  x[3]: "<U+6210><U+4EA4>    "
  y[3]: "\"\\u6210\\u4ea4\""
  
  x[4]: "<NA>    "
  y[4]: "<NA>          "
  
  == testthat results  ===========================================================
  OK: 135 SKIPPED: 2 FAILED: 2
  1. Failure: output test (@test-format_character.R#70) 
  2. Failure: output test (@test-format_character.R#71) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Component "loadedOnly": Component 4: Component 1: 1 string mismatch
  Component "loadedOnly": Component 4: Component 2: 1 string mismatch
  Component "loadedOnly": Component 4: Component 3: 1 string mismatch
  Component "loadedOnly": Component 4: Component 4: 1 string mismatch
  ...
  Correct session information is set in provenance
  
  Provenance hash a generated on b with c.
  == testthat results  ===========================================================
  OK: 1191 SKIPPED: 2 FAILED: 2
  1. Failure: provenance (@test-provenance.R#7) 
  2. Failure: provenance (@test-provenance.R#11) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Overview.Rmd' failed with diagnostics:
path for html_dependency not found: 
Execution halted
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.eg.db'
  'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db' 'org.Pf.plasmo.db'
  'org.Xl.eg.db'
Authors@R field gives persons with no valid roles:
  R Consortium [fnd]
Running examples in 'psychmeta-Ex.R' failed
The error most likely occurred in:

> ### Name: correct_d
> ### Title: Correct _d_ values for range restriction and/or measurement
> ###   error
> ### Aliases: correct_d
> 
> ### ** Examples
> 
> ## Correction for measurement error only
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
    dgy   dgp   dGy   dGp
1 0.458 0.516 0.512 0.578
> correct_d(correction = "meas", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = NULL, pa = .5, n1 = 100, n2 = 200)

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
  value CI_LL_95 CI_UL_95   n n_effective
1 0.595      0.3    0.912 300         183
> 
> ## Correction for direct range restriction in the continuous variable
> correct_d(correction = "uvdrr_y", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)
Error in indirect_rr | rxxa_consistency : 
  operations are possible only for numeric, logical or complex types
Calls: correct_d -> correct_r -> correct_r_uvdrr
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R     1.2Mb
    doc   2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
Running 'testthat.R' [162s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  13: new("dfmSparse", Matrix(as.matrix(x), sparse = TRUE))
  14: initialize(value, ...)
  15: initialize(value, ...)
  16: callNextMethod()
  17: .nextMethod(.Object = .Object, ... = ...)
  18: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  19: asMethod(object, Class, value)
  20: slot(value, what)
  
  testthat results ================================================================
  OK: 1574 SKIPPED: 20 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [167s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  13: new("dfmSparse", Matrix(as.matrix(x), sparse = TRUE))
  14: initialize(value, ...)
  15: initialize(value, ...)
  16: callNextMethod()
  17: .nextMethod(.Object = .Object, ... = ...)
  18: `as<-`(`*tmp*`, Classi, value = <S4 object of class structure("dtCMatrix", package = "Matrix")>)
  19: asMethod(object, Class, value)
  20: slot(value, what)
  
  testthat results ================================================================
  OK: 1574 SKIPPED: 20 FAILED: 1
  1. Error: dfm_lookup raises error when dictionary has multi-word entries (@test-dfm_lookup.R#82) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
    po    2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      2.9Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [87s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > 
  > test_check("rdomains")
  -- 1. Error: dmoz cat (@test-dmoz-cat.R#5)  ------------------------------------
  HTTP error 404.
  1: get_dmoz_data() at testthat/test-dmoz-cat.R:5
  2: curl_download("https://github.com/soodoku/domain_classifier/blob/master/rdomains/data-raw/dmoz/dmoz_domain_category.zip?raw=true", 
         tmp)
  
  Shallalist Data saved to the following destination: ./ 
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Error: dmoz cat (@test-dmoz-cat.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/redcapAPI.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rsolr'
Error in re-building vignettes:
  ...
Quitting from lines 134-152 (arrays.Rmd) 
Error: processing vignette 'arrays.Rmd' failed with diagnostics:
ImportError: Module use of python34.dll conflicts with this version of Python.

Detailed traceback: 
  File "<string>", line 1, in <module>
  File "D:\Compiler\python\lib\site-packages\numpy\__init__.py", line 185, in <module>
    from . import add_newdocs
  File "D:\Compiler\python\lib\site-packages\numpy\add_newdocs.py", line 13, in <module>
    from numpy.lib import add_newdoc
  File "D:\Compiler\python\lib\site-packages\numpy\lib\__init__.py", line 8, in <module>
    from .type_check import *
  File "D:\Compiler\python\lib\site-packages\numpy\lib\type_check.py", line 11, in <module>
    import numpy.core.numeric as _nx
  File "D:\Compiler\python\lib\site-packages\numpy\core\__init__.py", line 6, in <module>
    from . import multiarray
Execution halted
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
.install_system_dependencies : <anonymous>: no visible global function
  definition for 'unzip'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'menu'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'download.file'
as.GParamSpec: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

Compiled code should not call entry points which might terminate R nor
write to stdout/stderr instead of to the console, nor 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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rmetasim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.4Mb
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.Rcheck/00install.out' for details.
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

> ### Name: RSVGTipsDevice
> ### Title: A SVG Graphics Driver with dynamic tips
> ### Aliases: RSVGTipsDevice
> ### Keywords: device package
> 
> ### ** Examples
> 
> library("RSVGTipsDevice")
> sessionInfo()
R version 3.3.0 beta (2016-04-13 r70476)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6002) Service Pack 2

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

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

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Authors@R field gives persons with no valid roles:
  ERC Grant Agreement number 336167 - the CHAI Project [fnd]
  Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
  Kara  Woo [rev] (Kara Woo reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       1.8Mb
    projects   2.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/s2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/SASxport.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/selectiveInference.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.xml_missing', '[.xml_nodeset', '[[.xml_missing', 'xml_attr<-.xml_missing', 'xml_attr<-.xml_node', 'xml_attr<-.xml_nodeset', 'xml_attrs<-.xml_missing', 'xml_attrs<-.xml_node', 'xml_attrs<-.xml_nodeset', 'xml_name<-.xml_missing', 'xml_name<-.xml_node', 'xml_name<-.xml_nodeset', 'xml_text<-.xml_missing', 'xml_text<-.xml_node', 'xml_text<-.xml_nodeset', 'as.character.xml_document', 'as.character.xml_missing', 'as.character.xml_node', 'as.character.xml_nodeset', 'as_list.xml_missing', 'as_list.xml_node', 'as_list.xml_nodeset', 'as_xml_document.character', 'as_xml_document.connection', 'as_xml_document.list', 'as_xml_document.raw', 'as_xml_document.response', 'as_xml_document.xml_document', 'as_xml_document.xml_node', 'as_xml_document.xml_nodeset', 'format.xml_node', 'is.na.xml_missing', 'is.na.xml_node', 'is.na.xml_nodeset', 'nodeset_apply.xml_document', 'nodeset_apply.xml_missing', 'nodeset_apply.xml_node', 'nodeset_apply.xml_nodeset', 'print.xml_document', 'print.xml_missing [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.3/selectr.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: D:/temp/Rtmp0cLr4b/R.INSTALL1229c669536e1/sharpr2/man/sharpr2-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/sharpr2.Rcheck/00install.out' for details.
prepare_Rd: sharpr2-package.Rd:1: All text must be in a section
Package required and available but unsuitable version: 'tools'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.2Mb
Running examples in 'speaq-Ex.R' failed
The error most likely occurred in:

> ### Name: HMDBsearchR
> ### Title: Submit 1H NMR peaks to HMDB for compound search
> ### Aliases: HMDBsearchR
> 
> ### ** Examples
> 
> HMDBsearchR(peakVector = c(3.2, 3.38), ppmTol = 0.2, returnURL = TRUE)
Warning in request_GET(session, url) : Gateway Timeout (HTTP 504).
Error in open.connection(x, "rb") : HTTP error 502.
Calls: HMDBsearchR -> <Anonymous> -> <Anonymous> -> read_html.default
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    include   8.3Mb
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "VignetteforSTPGA.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.3.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.3.3/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'VignetteforSTPGA.ltx' failed with diagnostics:
running 'texi2dvi' on 'VignetteforSTPGA.ltx' failed

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

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

Execution halted
Authors@R field gives persons with no valid roles:
  Scott  Chamberlin [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  The following object is masked from 'package:testthat':
  
      skip
  
  > 
  > test_check("swirlify")
  -- 1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R
  all(correct_output %in% readLines(file.path(path, "test.log"))) isn't true.
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 1 FAILED: 1
  1. Failure: test_lesson() passes with well-formed lesson (@test_test_lesson.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sybilSBML.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 27-29 (HierarchicalModels.Rmd) 
Error: processing vignette 'HierarchicalModels.Rmd' failed with diagnostics:
Could not find feasible matrix. Subrectangle in row(s) 5 and column(s) 5 violates existence condition.
Execution halted
makeCircles: no visible global function definition for 'quantile'
targetDiagram: no visible global function definition for 'as.formula'
targetDiagram: no visible global function definition for 'modifyList'
targetDiagram: no visible global function definition for 'extendrange'
tdStats : sdo: no visible global function definition for 'sd'
tdStats : sdm: no visible global function definition for 'sd'
tdStats : r2: no visible global function definition for 'cor'
Undefined global functions or variables:
  as.formula cor extendrange modifyList quantile sd
Consider adding
  importFrom("grDevices", "extendrange")
  importFrom("stats", "as.formula", "cor", "quantile", "sd")
  importFrom("utils", "modifyList")
to your NAMESPACE file.
Package required and available but unsuitable version: 'quanteda'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages required and available but unsuitable versions:
  'parallel' 'phyloseq' 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [43s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })
  9: expr_type_of(.x)
  10: typeof(x)
  11: duplicate(quo)
  
  == testthat results  ===========================================================
  OK: 149 SKIPPED: 2 FAILED: 5
  1. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#15) 
  2. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#17) 
  3. Failure: Test returns tibble with correct rows and columns. (@test_tq_get_key_stats.R#19) 
  4. Error: Test error on invalid data inputs. (@test_tq_mutate.R#142) 
  5. Error: Test error on invalid data inputs. (@test_tq_transmute.R#121) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  -- 2. Error: can augment an stm output (@test-stm-tidiers.R#59)  ---------------
  no applicable method for 'as.dfm' applied to an object of class "c('dgCMatrix', 'CsparseMatrix', 'dsparseMatrix', 'generalMatrix', 'dCsparseMatrix', 'dMatrix', 'sparseMatrix', 'compMatrix', 'Matrix', 'xMatrix', 'mMatrix', 'Mnumeric', 'replValueSp')"
  1: augment(stm_model, dat) at testthat/test-stm-tidiers.R:59
  2: augment.STM(stm_model, dat)
  3: cast_dfm(data, document, term, value)
  4: quanteda::as.dfm(m)
  
  == testthat results  ===========================================================
  OK: 218 SKIPPED: 0 FAILED: 2
  1. Error: Can cast tables into a sparse dfm (@test-sparse-casters.R#73) 
  2. Error: can augment an stm output (@test-stm-tidiers.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "book"
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 896 rows containing non-finite values (stat_bin).
Loading required package: NLP

Attaching package: 'NLP'

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

    annotate

Quitting from lines 95-115 (tidying_casting.Rmd) 
Error: processing vignette 'tidying_casting.Rmd' failed with diagnostics:
no applicable method for 'as.dfm' applied to an object of class "c('dgCMatrix', 'CsparseMatrix', 'dsparseMatrix', 'generalMatrix', 'dCsparseMatrix', 'dMatrix', 'sparseMatrix', 'compMatrix', 'Matrix', 'xMatrix', 'mMatrix', 'Mnumeric', 'replValueSp')"
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    level type   token
    <int> <chr>  <chr>
  1     0 number 1    
  -- 1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4)  
  xlsx_sheet_names("./examples.xlsx")[1:2] not equal to c("Sheet1", "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°").
  1/2 mismatches
  x[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.Â£Â¹Ã·Â¦Â°"
  y[2]: "1~`!@#$%^&()_-+={}|;\"'<,>.£¹÷¦°"
  
  == testthat results  ===========================================================
  OK: 327 SKIPPED: 0 FAILED: 1
  1. Failure: sheet names are returned correctly (@test-xlsx_sheet_names.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/treethresh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs        4.1Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("urltools")
  -- 1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Hinrichtung_auf_dem_AltstÃ¤dter_Ring.JPG/120px-Hinrichtung_auf_dem_AltstÃ
  x[1]: ¤dter_Ring.JPG"
  y[1]: "Hinrichtung_auf_dem_Altstädter_Ring.JPG/120px-Hinrichtung_auf_dem_Altstäd
  y[1]: ter_Ring.JPG"
  
  == testthat results  ===========================================================
  OK: 157 SKIPPED: 0 FAILED: 1
  1. Failure: Check decoding and encoding are equivalent (@test_encoding.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Error in (function (x)  : 
    no function to return from, jumping to top level
  == testthat results  ===========================================================
  OK: 90 SKIPPED: 0 FAILED: 8
  1. Error: summary extract works with lines and polygons (@test_extract.R#26) 
  2. Error: (unknown) (@test_extract.R#8) 
  3. Error: summary extract works with lines and polygons (@test_extract.R#26) 
  4. Error: (unknown) (@test_extract.R#8) 
  5. Error: summary extract works with lines and polygons (@test_extract.R#26) 
  6. Error: (unknown) (@test_extract.R#8) 
  7. Error: summary extract works with lines and polygons (@test_extract.R#26) 
  8. Error: (unknown) (@test_extract.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Error in re-building vignettes:
  ...
Loading required package: maps
Loading required package: tuneR
Loading required package: seewave
Quitting from lines 102-109 (warbleR_workflow_phase1.Rmd) 
Error: processing vignette 'warbleR_workflow_phase1.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Database file #2: knitcitations.bib
Warning--I didn't find a database entry for "R_Core_Team_2017"
Warning--I didn't find a database entry for "Muller_2016"
Warning--I didn't find a database entry for "Eddelbuettel_2011"
Warning--I didn't find a database entry for "Eddelbuettel_2013"
Warning--I didn't find a database entry for "Eddelbuettel_2017"
Warning--I didn't find a database entry for "Muller_2017"
Warning--I didn't find a database entry for "Mersmann_2015"
Warning--I didn't find a database entry for "Dewey_2017"
Warning--I didn't find a database entry for "Tille_2016"
Warning--I didn't find a database entry for "Bischl_2015"
Warning--I didn't find a database entry for "Wickham_2017"
Warning--I didn't find a database entry for "Wickham_2017a"
Warning--I didn't find a database entry for "Wickham_2009"
Warning--I didn't find a database entry for "Sharpsteen_2016"
Warning--I didn't find a database entry for "Xie_2017"
Warning--I didn't find a database entry for "Xie_2015"
Warning--I didn't find a database entry for "Xie_2014"
Warning--I didn't find a database entry for "Allaire_2017"
Warning--I didn't find a database entry for "Allaire_2017a"
(There was 1 error message)
Warning: running command '"bibtex" "wrswoR.aux"' had status 1
Error: processing vignette 'wrswoR.Rmd' failed with diagnostics:
Failed to build the bibliography via bibtex
Execution halted
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "# ç\u008f¾è¡ã\u0081®å­¦æ ¡ææ³ã\u0081§ã\u0081¯ã\u0081è±èªã\u0081«ã\
  y[1]: u0081ããã\u0081ã\u0081ªãç®çèªã\u008dãè£èªã\u008d"
  
  -- 2. Failure: UTF-8 is OK (@test.R#78)  ---------------------------------------
  length(op) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: UTF-8 is OK (@test.R#66) 
  2. Failure: UTF-8 is OK (@test.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Running 'testthat.R' [108s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  x[1]: "Specials:\n  problem method type       data        modified\n    <dbl> <c
  x[1]: hr>  <chr>      <list>      <lgl>   \n1    3.00 vpc    continuous <list [2
  x[1]: 0]> F       "
  y[1]: "Specials:\n  problem method       type        data modified\n    <dbl>  <
  y[1]: chr>      <chr>      <list>    <lgl>\n1       3    vpc continuous <list [2
  y[1]: 0]>    FALSE"
  
  == testthat results  ===========================================================
  OK: 526 SKIPPED: 0 FAILED: 3
  1. Failure: Check list_data returns a proper message (@test-console_outputs.R#43) 
  2. Failure: Check list_files returns a proper message (@test-console_outputs.R#47) 
  3. Failure: Check list_special returns a proper message (@test-console_outputs.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/xptr.Rcheck/00install.out' for details.
Running examples in 'yCrypticRNAs-Ex.R' failed
The error most likely occurred in:

> ### Name: annotationsSet
> ### Title: Create a geneAnnotation object.
> ### Aliases: annotationsSet
> 
> ### ** Examples
> 
> annotationsSet()
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  scerevisiae_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: annotationsSet -> <Anonymous> -> useDataset
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/abcdeFBA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rglpk’ ‘corrplot’ ‘lattice’ ‘rgl’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1/1 mismatches
  x[1]: "\"a\"e\"i\"o\"u\"A\"E\"I\"O\"U\"y"
  y[1]: "aeiouAEIOUy"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 4
  1. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#30) 
  2. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#32) 
  3. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#33) 
  4. Failure: rm_accent is the converted version of a string with all non-ASCII characters removed. (@test-rm_accent.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    2.9Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'acceptance_sampling_manual.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          K^^[]^^W>o<fc>h^^Zj<93>^(E<94><98><e1>B<a1><85>`^^GfW<b0>q<91><b5><bb>v<e5><da>MW]<b9><95><ae>tӮ<eb><bf><e0><aa>Y<94>B<b2>H^^P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...߾<bd>s<e7>N6<9b><c5>O)<a5><94>rmm<cd>0<8c>B<a1> <a5>dX<ee><ed><ed><e1><95>eY<8f>^^^=<da><dd>ݽ}
                                                  <fb><f6><f2><f2><b2>R^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.20 ...ZYYY[[^^C2<9f>?^^?<8e>-<87><9f><d9>l<d6>4<cd>l6<fb><e2><c5><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ACSN-vignette.Rmd appears to be an R Markdown v2 document.
Quitting from lines 70-71 (ACSN-vignette.Rmd) 
Error: processing vignette 'ACSN-vignette.Rmd' failed with diagnostics:
the table must have a header (column names)
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/adiv.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'AER.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<bc>Aι<ee>M<ea>^^X<84>^^PA^^P<e8><ba>.<84>H$^^R<ba><ae>æ^^GA<d0><ed>v<87>t\<a8>
                                                  <ff><f9><f3><e7>l6[<af><d7>e'D<f4><ea>ի<d5><d5>UT^^[<c3>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.21 ...ޯP<af><d7><d5>`|H@<f8><93>V<bf>^^Q<c8><c9>9<97>S^^[<86><a1><a6>i(<f7>}^^_<fb>/9<cd>x<f6>}
                                                  <9f><88>@`<c6>؟^^?<be><fb><e3><8f>^^?9N<c3>0d<c3>0<9f>g...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.24 ...^^?<d7>2^^L^^F۷<d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘AFM-Ex.R’ failed
The error most likely occurred in:

> ### Name: evaluateVariogramModels
> ### Title: evaluateVariogramModels method to evaluate the basic variogram
> ###   models
> ### Aliases: evaluateVariogramModels
> ###   evaluateVariogramModels,AFMImageVariogramAnalysis-method
> 
> ### ** Examples
> 
> library(AFM)
> 
> data("AFMImageOfRegularPeaks")
> # take an extract of the image to fasten the calculation      
> AFMImage<-extractAFMImage(AFMImageOfRegularPeaks, 40, 40, 32)
[1] "40 40 31 40 71 40 71"
> # e.g. AFMImage@fullfilename<-"/users/ubuntu/AFMImageOfRegularPeaks-extract.txt"
> AFMImage@fullfilename<-paste(tempdir(), "AFMImageOfRegularPeaks-extract.txt", sep="/")
>  
> AFMImageAnalyser<-AFMImageAnalyser(AFMImage)
Warning in data.table(lib = c("AFM", "gstat", "fractaldim", "fftwtools"),  :
  Item 1 is of size 4 but maximum size is 5 (recycled leaving remainder of 1 items)
>  
>  # Variogram analysis 
> sampleFitPercentage<-3.43/100
> variogramAnalysis<-AFMImageVariogramAnalysis(sampleFitPercentage)
> variogramAnalysis@omnidirectionalVariogram<- 
+               AFM::calculateOmnidirectionalVariogram(AFMImage=AFMImage,
+                                                      AFMImageVariogramAnalysis=variogramAnalysis)
[1] "using automatic width of 1"
[1] "calculating omnidirectional variogram using width of 1 ..."
Error in CRS("+init") : no colon in init= string
Calls: <Anonymous> -> CRS
Execution halted
Package required and available but unsuitable version: ‘miscF’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘timetk’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/alphavantager.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'amei.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...߾<8d><c6>L&<c3>9<ff><ee><bb><ef>^^Xc_~<f9><e5><f5><eb><d7>s<b9>^^\<ba>q<ce><ef>޽<fb><c5>^^W_\<bc>
                                                  xq~~~aa!<9b><cd><ce><ce><ce>b<e4>\.W<af><d7><c7><c7><c7>^^Y...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...<9b>^^L<c7>0<8f>Z<ad><86><bb><b2><85><88>8<e7>^^@<92><aa><aa><a6>i<a2><b1>X,<fa><be><8f>G<d0><e2><fb>~4|Å\D
                                                  Ƙ<bc><85><b7><d4>j<b5>v<e6><dc>^^Y8;<c5>ի<8d>ȨSp^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <c3>0<96><97><97><af>\<b9>
             <e2><ba>.F+^^T^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.24
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/analogueExtra.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/animalTrack.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    %>%

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

    id

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

    escape, explain

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 56-58 (ANLP_Documentation.Rmd) 
Error: processing vignette 'ANLP_Documentation.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/tokenizers/NGramTokenizer : Unsupported major.minor version 51.0
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AnnotationBustR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyannot : annotlist: no visible global function definition for
  ‘read.table’
annot : annotlist: no visible global function definition for
  ‘write.table’
annot: no visible global function definition for ‘flush.console’
annot: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  flush.console read.table write.table
Consider adding
  importFrom("utils", "flush.console", "read.table", "write.table")
to your NAMESPACE file.
Packages required but not available: ‘BioInstaller’ ‘ngstk’

Package required and available but unsuitable version: ‘configr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AnthropMMD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Aoptbdtvc.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: Conversion from REAL(8) to default-kind COMPLEX(4) at (1) might loose precision, consider using the KIND argument
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/appell.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keykristen.colors: no visible global function definition for
  ‘colorRampPalette’
kristen.colors: no visible global function definition for ‘grey’
plot3d.points: no visible global function definition for ‘heat.colors’
plot3d.points: no visible global function definition for ‘plot’
ragged.image: no visible global function definition for ‘heat.colors’
ragged.image: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘grey’
scatterplot.density: no visible global function definition for ‘image’
scatterplot.density: no visible global function definition for ‘abline’
scatterplot.density: no visible global function definition for ‘lm’
scatterplot.density: no visible global function definition for ‘legend’
vertical.image.legend: no visible global function definition for ‘par’
vertical.image.legend: no visible global function definition for
  ‘image’
vertical.image.legend: no visible global function definition for ‘axis’
vertical.image.legend: no visible global function definition for ‘box’
Undefined global functions or variables:
  abline axis box colorRampPalette grey heat.colors image legend lm par
  plot
Consider adding
  importFrom("grDevices", "colorRampPalette", "grey", "heat.colors")
  importFrom("graphics", "abline", "axis", "box", "image", "legend",
             "par", "plot")
  importFrom("stats", "lm")
to your NAMESPACE file.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  ── 1. Error: (unknown) (@test-argparse.R#24)  ──────────────────────────────────
  Couldn't find a sufficient Python binary. If you haven't installed the Python dependency yet please do so. If you have but it isn't on the system path (as is default on Windows) please add it to path or set options('python_cmd'='/path/to/binary')  or set the PYTHON, PYTHON2, or PYTHON3 environmental variables. Python must be at least version 3.0  Python must have access to the modules: argparse, json | simplejson
  1: options(python_cmd = find_python_cmd(minimum_version = "3.0", required_modules = c("argparse", 
         "json | simplejson"))) at testthat/test-argparse.R:24
  2: find_python_cmd(minimum_version = "3.0", required_modules = c("argparse", "json | simplejson"))
  3: stop(error_message)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-argparse.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ARTP2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ASIP.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  
  Attaching package: 'llama'
  
  The following object is masked from 'package:BBmisc':
  
      normalize
  
  > test_check("aslib")
  Loading required package: aslib
  Error in .jnew("weka/core/Instances", .jcast(reader, "java/io/Reader")) : 
    java.lang.UnsupportedClassVersionError: weka/core/Instances : Unsupported major.minor version 51.0
  Calls: test_check ... eval -> parseASScenario -> read.arff -> .jnew -> .External
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AssocAFC.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/asus.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/AtelieR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘trtf’
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, handled)
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_stack_thresh.R#1) 
  2. Error: (unknown) (@test_thresh.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   1.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bamboo.Rcheck/00install.out’ for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Error in re-building vignettes:
  ...
  input string 487 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'bartMachine.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o^^[<d5>^^V?uh<92>yJ=<b9><b4>/qG8q<86>V<a4>-JSy<c3>C<aa>^^\!<8b>%^^[^^T<84><c4>^^V<f5>^^O`<c3>6<cb>v^^A6^^H...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...T*e<9a><a6>eY<f1>u<92>R<fe><f0><c3>^^O<b6>m^^O^^O^^O<a3><f4><e7><9f>^^?<fe>裏<ae>\<b9>
                                                  <92>L&<e3><f1>x<c0><b8><ab><cf>^^Gݸq<a3>X,nV:55<b5><b3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...ȣG<8f><c0><86>eY<9f>}<f6>^^Y$MU <a2>^^O?<fc>0<9d>N^^O^^O^^O<ef>r
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.7Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/baseballDBR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BASiNET.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 8-9 (./child/ex5-2.Rnw) 
Quitting from lines 44-44 (./child/ex5-2.Rnw) 
Error: processing vignette 'article2-vignette.Rnw' failed with diagnostics:
cannot open connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bayesCL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BayesCR.Rcheck/00install.out’ for details.
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  10.2Mb
Package unavailable to check Rd xrefs: ‘mritc’
installed size is 54.5Mb
  sub-directories of 1Mb or more:
    libs  53.8Mb
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  18.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BayesTwin.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Running examples in ‘BCEs0-Ex.R’ failed
The error most likely occurred in:

> ### Name: bces0
> ### Title: Bayesian Cost-Effectiveness models in the presence of structural
> ###   zeros
> ### Aliases: bces0 bces0.default
> ### Keywords: JAGS Markov Chain Monte Carlo Bayesian models for
> ###   cost-effectiveness analysis
> 
> ### ** Examples
> 
> data(acupuncture)
> m <- bces0(data,dist.c="gamma",dist.e="beta",n.iter=1000,n.burnin=500,n.chains=2)
Installing package into ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BCEs0.Rcheck’
(as ‘lib’ is unspecified)
Error in contrib.url(repos, "source") : 
  trying to use CRAN without setting a mirror
Calls: bces0 -> bces0.default -> install.packages -> contrib.url
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BClustLonG.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bcmaps.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘beadarrayExampleData’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'beanplot.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^S<dd>^^Z^^?<9a><be><a1>w@frn<ef><d5><da>2<a6>^^\<f0><f6><95>+i<a1><f0>.^^DM<c1><e8>Fp<d7>U<f7><ae><dd>	<ae><dc><f6>/<90>׽<a2><88>.<b2>m^^V
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<cd>qb-s<fd>H<ee><e2>w<f3>0o?<92><c6>&jj~<8b>rr<be><e6><s~<e7><f9>8<e7>L^^G<ea><f5>:<9d>\D
                                                  ~<f4>^^@<ba><8b><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd><8c><be>x<bd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.19 ...<d3>D<ce><ce><ce>N"<91><d0>ZW<ab>U<d3>4<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.2Mb
Invalid MIT-MAGIC-COOKIE-1 keybeqi2: no visible global function definition for ‘na.omit’
beqi2: no visible global function definition for ‘browseURL’
readAMBI: no visible global function definition for ‘read.csv’
readBEQI: no visible global function definition for ‘read.csv’
readERF: no visible global function definition for ‘read.csv’
readTWN: no visible global function definition for ‘read.csv’
read_ITI_FIBI: no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  browseURL na.omit read.csv
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "browseURL", "read.csv")
to your NAMESPACE file.
Running examples in ‘berryFunctions-Ex.R’ failed
The error most likely occurred in:

> ### Name: normalizePathCP
> ### Title: normalizePath Cross Platform
> ### Aliases: normalizePathCP
> ### Keywords: file
> 
> ### ** Examples
> 
> 
> normalizePath  ("doesnotexist.file", mustWork=FALSE) # on linux not full path
[1] "doesnotexist.file"
> normalizePathCP("doesnotexist.file") # full path on all platforms
[1] "doesnotexist.file"
> 
> checknp <- function(a,b=a,d=getwd()) 
+   {
+   aa <- normalizePathCP(a)
+   bb <- if(d=="") b else paste0(d,"/",b)
+   if(aa != bb) stop("'", a, "' -> '", aa, "', should be '",bb, "'.")
+   aa
+   }
> 
> checknp("notexist.file")
Error in checknp("notexist.file") : 
  'notexist.file' -> 'notexist.file', should be '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/berryFunctions.Rcheck/notexist.file'.
Execution halted
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'betareg-ext.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...x(^^T<f2>}?^^R<89>^^L,<e7><d3><e2><ff>۴<^^Q<f0>Ȝs<d7>uM<d3>ܩZ<cb>[<fc><f4>}
                                                  ?^^T^^J
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<9a>f<ad>V<b3>,<eb><db>o<bf>=z<f4><e8><c4>ĄeYB^^HM<d3>^^P3p<ce>QF<83><9d>D^^Q]<8c>^
                                                  6<9b><cd>d2B^^H<c7>q^^P<be><98><a6>iY^^V^^Q#...
! Extra }, or forgotten $.
l.18 ...t<ee>ܹF<a3><c1>^^X[XX0M3<91>H^^P<d1><db>o<bf>m<9a><e6><f0><f0>0^^Q<f9><be><af>$A<d9><f7>}
                                                  <df><f7>5<ad>#<ce
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/BETS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/biclique.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   4.5Mb
installed size is 28.9Mb
  sub-directories of 1Mb or more:
    libs  28.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Error in re-building vignettes:
  ...
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 3]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 1]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in is.na(verts[, 2]) :
  is.na() applied to non-(list or vector) of type 'NULL'
Warning in normalizePath(f2) :
  path[1]="./webshot12a377e723c42.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot12a377e723c42.png': No such file or directory
Quitting from lines 240-243 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.0Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   6.4Mb
Running examples in ‘Biocomb-Ex.R’ failed
The error most likely occurred in:

> ### Name: Biocomb-package
> ### Title: Tools for Data Mining
> ### Aliases: Biocomb-package Biocomb
> ### Keywords: package feature selection classification information gain
> ###   Relative cost curves HUM roc auc
> 
> ### ** Examples
> 
> data(data_test)
> # class label must be factor
> data_test[,ncol(data_test)]<-as.factor(data_test[,ncol(data_test)])
> 
> # Perform the feature selection using the fast correlation-based filter algorithm
> disc="MDL"
> threshold=0.2
> attrs.nominal=numeric()
> out=select.fast.filter(data_test,disc.method=disc,threshold=threshold,
+ attrs.nominal=attrs.nominal)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: select.fast.filter ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Package required and available but unsuitable version: ‘configr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bios2mds.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bioset.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/birdring.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/birtr.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘GOSemSim’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because profiling.Rmd appears to be an R Markdown v2 document.
Quitting from lines 40-46 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blandr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blastula.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
installed size is 30.5Mb
  sub-directories of 1Mb or more:
    libs  29.5Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/blockmodeling.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
This data.table install has not detected OpenMP support. It will work but slower in single threaded mode.
Package suggested but not available for checking: ‘RcppTOML’
installed size is 31.3Mb
  sub-directories of 1Mb or more:
    libs  31.1Mb
installed size is 243.0Mb
  sub-directories of 1Mb or more:
    include    2.7Mb
    lib      240.0Mb
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    libs  46.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/bpca.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 445 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'BradleyTerry.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<a3>B<88><b9><b9><b9><8f>?<fe>8<91>H<fc><f1><c7>^^_~<bf>^^_<e8>D<d3><b4>^^N<b9><cd><ce><ce>>}<fa><b4><bf><bf><bf>^
                                                  <af>^^?<f8>ᇉDb|||mm-^^^<8f>^^_y<86>G...
! Undefined control sequence.
l.19 <a1><cd>97M3^^V<8b>u<ce>gO<ba><f0><bd><b3>L<e7>\<bc>
                           6<a1>%<95>J<9d><ce><<8e>C^^G`<d7>s<ee>{'<89>9^^O&$D<e3><e3><e3>><9f><af>V<ab><85>B<a1>n<a7>t<ee><b5><f7><d7>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten $.
l.23 ...B<88><9d><9d>^^]<84>iDs<c3>0B<a1><90><db>^^Uc<b1><98>a^^X<96>e^^E<83>A<8f><c7>S*<95><9e>>}
                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘BrailleR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breakfast.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/breathtestcore.Rcheck/00install.out’ for details.
Package required but not available: ‘breathtestcore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
jg.countAlignedMReads: no visible global function definition for
  ‘idxstatsBam’
Undefined global functions or variables:
  idxstatsBam
installed size is 26.7Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
Running the tests in ‘tests/test_all.R’ failed.
Last 13 lines of output:
  1. Failure: Gaussian approximation results of bssm and KFAS coincide (@test_approx.R#9) 
  2. Failure: Gaussian approximation results of bssm and KFAS coincide (@test_approx.R#11) 
  3. Failure: Gaussian approximation results of bssm and KFAS coincide (@test_approx.R#13) 
  4. Error: Gaussian approximation results of bssm and KFAS coincide (@test_approx.R#14) 
  5. Failure: results for poisson GLM are equal to glm function (@test_approx.R#37) 
  6. Failure: results for poisson GLM are equal to glm function (@test_approx.R#39) 
  7. Error: results for poisson GLM are equal to glm function (@test_approx.R#40) 
  8. Failure: results for binomial GLM are equal to glm function (@test_approx.R#57) 
  9. Failure: results for binomial GLM are equal to glm function (@test_approx.R#59) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘c3net-Ex.R’ failed
The error most likely occurred in:

> ### Name: c3net
> ### Title: All in one function to infer network with C3NET
> ### Aliases: c3net
> ### Keywords: misc
> 
> ### ** Examples
> 
> data(expdata)
> data(truenet)
> 
> net <- c3net(expdata, network=TRUE)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: c3net ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CAISEr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-13, (SVN revision 686)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-5 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Canopy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cape.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/capm.Rcheck/00install.out’ for details.
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

> ### Name: carpools.hit.overview
> ### Title: Analysis: Analysis of pooled CRISPR screening data using a
> ###   Wilcoxon Test
> ### Aliases: carpools.hit.overview
> ### Keywords: ~Analysis
> 
> ### ** Examples
> 
> data(caRpools)
> 
> data.wilcox = stat.wilcox(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1, fullmatchcolumn=2,
+   normalize=TRUE, norm.fun=median, sorting=FALSE, controls="random",
+   control.picks=NULL)
> 
> 
> data.deseq = stat.DESeq(untreated.list = list(CONTROL1, CONTROL2),
+   treated.list = list(TREAT1,TREAT2), namecolumn=1,
+   fullmatchcolumn=2, extractpattern=expression("^(.+?)(_.+)"),
+   sorting=FALSE, filename.deseq = "ANALYSIS-DESeq2-sgRNA.tab",
+   fitType="parametric")
Error in `rownames<-`(`*tmp*`, value = c("CTRL", "CTRL", "TREAT", "TREAT" : 
  duplicate rownames not allowed
Calls: stat.DESeq -> <Anonymous> -> rownames<- -> rownames<-
Execution halted
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'CaRpools.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because CaRpools.Rmd appears to be an R Markdown v2 document.
Quitting from lines 1875-1881 (CaRpools.Rmd) 
Error: processing vignette 'CaRpools.Rmd' failed with diagnostics:
duplicate rownames not allowed
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/catcont.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cati.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/catSurv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CATTexact.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'causaleffect.ltx' failed with diagnostics:
Running 'texi2dvi' on 'causaleffect.ltx' failed.
LaTeX errors:
! Undefined control sequence.
l.81 \DOI
         {10.18637/jss.v076.i12}
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
Execution halted
Running examples in ‘causalMGM-Ex.R’ failed
The error most likely occurred in:

> ### Name: loadSampleData
> ### Title: Load Sample Dataset
> ### Aliases: loadSampleData
> 
> ### ** Examples
> 
> library(rJava)
> mgm_init()
> ds <- loadSampleData()
Error in .jfindClass(as.character(class)) : class not found
Calls: loadSampleData -> J -> jclassName -> .jfindClass
Execution halted
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some ‘make’ programs ignore lines not ending in LF.
The following files look like leftovers/mistakes:
  ‘Causata-vignette.log’
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  ‘figure’
Please remove from your package.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cdcsis.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybw: no visible global function definition for ‘optimize’
Undefined global functions or variables:
  optimize
Consider adding
  importFrom("stats", "optimize")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cems.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 490 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 491 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 499 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ChainLadder.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<e5>^^B=<e5>^^B=<e5>^^B=<e5>^^B=<e5>^^B=G<80>R<ca>^^X<9b><e6><89><ff>ʯI\TP
                                                  .<97>5M^^C^^@Ji<a1>P(<97>ˌ<b1>@ ^^P<8b><c5>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 ...<e5><e2><a7>xNc~<fe><81>^^P<d2><ef><f7>E^^\<8b>ņ{<b3>^^Y^^N<9c><9f>r1<86><ba>-<95>J<b9>\<ce>
                                                  <b6><ed>t:<ad>i<9a>m<db>sss<af><af><af>;;;<b5>Z<ad>^<af><9b><a6><a9>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.35 x<9c><ed><9b><cf>k^^SM^^X<c7>?}c)Jh^^XP<90><96>T܃<a4>4<88>^^P<e8><a1>P^^T\<cf>
                                                <9e><fc>^^S<fc>^^[z-x<ca>^^_P<a4>z<f1>R^^T<aa><c7>^<ca>^^J
The control sequence at the end of the
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running the tests in ‘tests/test_changepoints.R’ failed.
Last 13 lines of output:
  [1] 89 10
  [1] 11 10
  [1] 90 10
  [1] 10 10
  [1] 77 10
  [1] 23 10
  > stopifnot(changepoints_mod@changepoints == 77)
  > 
  > # test rank one
  > res_ro = rank_one(scp_data, init, update_w=0.1, regularizer=0.1)
  > stopifnot(res_ro$tau == 56)
  Error: res_ro$tau == 56 is not TRUE
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/childsds.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/chillR.Rcheck/chillR/doc/hourly_temperatures.R':
invalid multibyte character in parser at line 26
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ciTools.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CLME.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clpAPI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clues.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/clusterSEs.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    colMeans, colSums, expand.grid, rowMeans, rowSums

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

Loading required package: moe430a.db
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘moe430a.db’
Loading required package: RankAggreg
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'clValid.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./clValid-022.pdf): PDF inclusion: required page 
does not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘WeightIt’
Running examples in ‘cobalt-Ex.R’ failed
The error most likely occurred in:

> ### Name: bal.tab.weightit
> ### Title: Balance Statistics for WeightIt Objects
> ### Aliases: bal.tab.weightit
> 
> ### ** Examples
> 
> library(WeightIt); data("lalonde", package = "cobalt")
Error in library(WeightIt) : there is no package called ‘WeightIt’
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.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATT and treated.
Note: estimand and s.d.denom not specified; assuming ATE and pooled.

Attaching package: 'MatchIt'

The following object is masked _by_ '.GlobalEnv':

    lalonde

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

    lalonde

Quitting from lines 241-252 (cobalt_basic_use.Rmd) 
Error: processing vignette 'cobalt_basic_use.Rmd' failed with diagnostics:
there is no package called 'WeightIt'
Execution halted
Running examples in ‘coindeskr-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_current_price
> ### Title: Extract Bitcoin Price Index from Coindesk API
> ### Aliases: get_current_price
> 
> ### ** Examples
> 
> get_current_price()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10021 milliseconds
Calls: get_current_price ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  4: get_current_price()
  5: httr::GET(url)
  6: request_perform(req, hu$handle$handle)
  7: request_fetch(req$output, req$url, handle)
  8: request_fetch.write_memory(req$output, req$url, handle)
  9: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: The output dataframe Type is  (@test-fun.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                     
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/comato.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyHopkins.index: no visible global function definition for ‘runif’
MBM.em: no visible global function definition for ‘runif’
PAM.cluster: no visible global function definition for ‘dist’
calculate.layout: no visible global function definition for ‘optim’
min.distance: no visible global function definition for ‘dist’
plot.conceptmap: no visible global function definition for ‘par’
plot.conceptmap: no visible global function definition for ‘plot’
plot.conceptmaps: no visible global function definition for ‘plot’
Undefined global functions or variables:
  dist optim par plot runif
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "dist", "optim", "runif")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cometExactTest.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘mogene10sttranscriptcluster.db’
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package required but not available: ‘RcppTOML’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/conjoint.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyConjoint: no visible global function definition for ‘dev.new’
Conjoint: no visible global function definition for ‘barplot’
caFactorialDesign: no visible global function definition for ‘cor’
caModel: no visible global function definition for ‘as.formula’
caModel: no visible global function definition for ‘lm’
caModel: no visible global function definition for ‘summary.lm’
caSegmentation: no visible global function definition for ‘kmeans’
caUtilities: no visible global function definition for ‘as.formula’
caUtilities: no visible global function definition for ‘lm’
caUtilities: no visible global function definition for ‘summary.lm’
partutilities: no visible global function definition for ‘as.formula’
partutilities: no visible global function definition for ‘lm’
partutils: no visible global function definition for ‘as.formula’
partutils: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘as.formula’
profsimcode: no visible global function definition for ‘lm’
profsimcode: no visible global function definition for ‘model.matrix’
totalutilities: no visible global function definition for ‘as.formula’
totalutilities: no visible global function definition for ‘lm’
totalutilities: no visible global function definition for
  ‘model.matrix’
utlsplot: no visible global function definition for ‘dev.new’
utlsplot: no visible global function definition for ‘barplot’
Undefined global functions or variables:
  as.formula barplot cor dev.new kmeans lm model.matrix summary.lm
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "barplot")
  importFrom("stats", "as.formula", "cor", "kmeans", "lm",
             "model.matrix", "summary.lm")
to your NAMESPACE file.
Packages required and available but unsuitable versions: ‘graphics’ ‘stats’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/corehunter.Rcheck/00install.out’ for details.
installed size is 24.5Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
Package required but not available: ‘standardize’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  ./bdsmatrix_stub.h:44:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
  ./bdsmatrix_stub.h:53:11: warning: incompatible pointer to integer conversion returning 'int *' from a function with result type 'int'; dereference with * [-Wint-conversion]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/coxme.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘cpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: cpa-package
> ### Title: Confirmatory Path Analysis through the d-sep tests
> ### Aliases: cpa-package
> ### Keywords: package
> 
> ### ** Examples
> 
> x <- cpa()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: cpa ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 31.0Mb
  sub-directories of 1Mb or more:
    libs  30.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'cplm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cb>^^L<8e><99><98>y<8b>#<8e><a6><98><d8>^^Fl^^By><b2><ac><f1>̹^^_g~<f7>|<dc>s<8f><db>\<d7>
                                                  <85><97><97><da>_<f4>^^D<9a>K-<f1><8e>3<b5><c4>;<ce><d4>^^R<ef>8<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...}<f6><d9>g<a3><a3><a3>B<88><c5><c5>ť<a5><a5>|>^^?<f9><f2>e|<a4>i^^Zʃ<bd><fd><f0><c3>^^O^^_}
                                                  <f4><91><a6>i׮]<db><c3>tݽS.<97><ab><f2><f4><c1><83>^^G<fb><e8><b3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ in
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 416 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 422 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'crch.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<cc><db><c0>H<bb>^^^<b7><d8>]<f1>^^\^^Y;-E<f9>)c<c9>O<8a><94><8b>9p<ca>^^A<e5><c2>-g<94>\<f3>
                                                  ^^W<e4><9a>?a9gOsC9^^RiFV^^T<81>4bl...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^X-&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><8d>3&<e2><fd>^^]J)<a5>^^T.N?<d5>Z<f3>}
                                                  <a5><94><d6><fa><ac><96><a7><db><f3><f5><fa><fa><fa><e9>.<b8><93>l?^^L<fe>5|<d3>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.15 .
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/crimCV.Rcheck/00install.out’ for details.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘predict’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘predict’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM: no visible global function definition for ‘predict’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
predict.kpbb: no visible global function definition for ‘predict’
uni.fpca: no visible global function definition for ‘predict’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm predict qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "predict", "qnorm", "rnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 707 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 708 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 716 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ctsem.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...@<be>^^TBZ<98><95><82><c4>E<d6><e2>F<dc>t<9d>^^?A<97>ŝ<9b><ee><cd><da>]w^^Aw<b3><e8>X\^^X
                                                  ^^Y^^LC@<83>:d:<ed><8b>^^U<da>kƚ<e3>[...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 L<97>\<d7>
         -^^V<8b><fc>^^W<85><cd><cd>͛7oR<8f>m<c1>%<a2>m^^X<86>^^G^^G^^Gx^^R<86><e1><d2><d2>^^R<bf><da><d8>ظr<e5>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...UU^^Q^^Oy nۧ<8c><92><f5><c0><d7>^^Fj2J<ea><fd><84><8c>=<e7>	<84><93><9d>V<ab><a5><aa>j<b9>\<86>
                                                  W<84><ab><94>R<96><cb>e<c7>q^^\<c7><f9>9<c7>x<ac><9c>qp^^N<d7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If y
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cudaBayesreg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/CVXR.Rcheck/00install.out’ for details.
installed size is 22.8Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/cytominer.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  7: http_error(HEAD(x, ...))
  8: HEAD(x, ...)
  9: request_perform(req, hu$handle$handle)
  10: request_fetch(req$output, req$url, handle)
  11: request_fetch.write_memory(req$output, req$url, handle)
  12: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 5 FAILED: 1
  1. Error: d3_dep-* src href is a valid url (@test_deps.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘d3r’
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DAKS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<8e><ad>^^_<b6><9c>X<ae><de>A<8c>fgf<e7><cd><fb><cc>{o޼<fd><c4><f7>}<ba><be>^^T<fa><d8>^^S<b8>\^^Z
                                                  <b3>7<ca>4fo<94>i<cc><de>(Ә<bd>Q<a6>1{<a3>L<ff>l<f6>LӔ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...|~gg端<be><c2><d0><f9>|<de>4<cd>l6<ab>:d^^X<c6>ӧO<f1><ee><cf>><fb>lgg<e7><e1>Ç<b9>\N
                                                  ^^H^^A<96>VVV<a4><94>h<a0><94>^^RB,//<f3>PD<f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...?<fe><f9><e7><f9><f9><f9>p8<bc><b2><b2><f2><dd>w<df>^^Y<86><a1><eb>z.<97><db><dc><dc><fc><fe><fb><ef>s<b9>^^\^^F\F
                                                  /DCDB^^W^^J
The control sequence at the end of the top 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DataExplorer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/datastructures.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/datasus.Rcheck/datasus/doc/Introduction_to_datasus.R':
invalid multibyte character in parser at line 50
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot9b12657d5480.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot9b12657d5480.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DBKGrad.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  42: build_sql("(", x, ")")
  43: vapply(dots(...), escape_expr, character(1))
  44: FUN(X[[i]], ...)
  45: eval_bare(x, .env)
  46: max(field, na.rm = TRUE) - min(field, na.rm = TRUE)
  47: min(field, na.rm = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 1
  1. Error: No error or warning when translated to SQL 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   5.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dc3net.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DCD.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘lumberjack’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-136 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'lumberjack'
Execution halted
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Invalid MIT-MAGIC-COOKIE-1 keyThere are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Running examples in ‘DecorateR-Ex.R’ failed
The error most likely occurred in:

> ### Name: DECORATE
> ### Title: Binary classification with DECORATE (Melville and Mooney, 2005)
> ### Aliases: DECORATE
> 
> ### ** Examples
> 
> 
> data(iris)
> y <- as.factor(ifelse(iris$Species[1:100]=="setosa",0,1))
> x <- iris[1:100,-5]
> dec <- DECORATE(x = x, y = y)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: DECORATE ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Running examples in ‘deisotoper-Ex.R’ failed
The error most likely occurred in:

> ### Name: deisotope
> ### Title: Deisotope a Mass Spectrum
> ### Aliases: deisotope
> 
> ### ** Examples
> 
> 
> x <- list(mZ = c(1, 2, 2.5, 3), intensity = rep(1, 4), pepmass=600, charge=2)
> 
> xd <- deisotope(dtoper <- deisotoper(), x)
Error in .jnew("ch.fgcz.proteomics.r.FeaturesBasedDeisotoping") : 
  java.lang.NoSuchMethodError: java.util.List.stream()Ljava/util/stream/Stream;
Calls: deisotope ... .jcall -> inherits -> deisotoper -> .jnew -> .External
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  9: value[[3L]](cond)
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, handled)
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 106 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-deisotoper.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Errors in running code in vignettes:
when running code in ‘deisotoper.Rnw’
  ...
+     4), pepmass = 600, charge = 2)

> x1 <- list(mZ = c(1.01, 2, 2.5, 3), intensity = rep(1, 
+     4), pepmass = 600, charge = 2)

> dtoper <- deisotoper()

  When sourcing 'deisotoper.R':
Error: java.lang.NoSuchMethodError: java.util.List.stream()Ljava/util/stream/Stream;
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rJava

Error: processing vignette 'deisotoper.Rnw' failed with diagnostics:
 chunk 9 
Error in .jnew("ch.fgcz.proteomics.r.FeaturesBasedDeisotoping") : 
  java.lang.NoSuchMethodError: java.util.List.stream()Ljava/util/stream/Stream;
Execution halted
Package required and available but unsuitable version: ‘ftsa’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
The following objects are masked from 'package:seriation':

    bluered, greenred

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

    lowess

Loading required package: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isNamespaceLoaded

Loading required package: rngtools
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
NMF - BioConductor layer [OK] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
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 925-927 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required and available but unsuitable version: ‘RWeka’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
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.

Attaching package: 'desctable'

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

    datatable

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

    IQR, chisq.test, fisher.test

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]="./webshot5fb33084ba6f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5fb33084ba6f.png': No such file or directory
Quitting from lines 66-73 (desctable.Rmd) 
Error: processing vignette 'desctable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    help   1.3Mb
    libs   1.2Mb
Package suggested but not available for checking: ‘dclone’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘dplR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘.get’ ‘InteractiveDetrending’ ‘RemoveTrend’
Running examples in ‘detrendeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: detrendeR-package
> ### Title: detrendeR - A Graphical User Interface to process and visualize
> ###   tree-ring data using R
> ### Aliases: detrendeR-package detrendeR
> ### Keywords: package
> 
> ### ** Examples
> 
> detrender()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: detrender ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘ijtiff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfcomb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dfmta.Rcheck/00install.out’ for details.
installed size is 43.6Mb
  sub-directories of 1Mb or more:
    libs  43.3Mb
Package required but not available: ‘ALL’

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

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

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Tktable") : Tcl package 'Tktable' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dgmbGui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/didrooRFM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/diffMeanVar.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/diffpriv.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/diffusr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/directPA.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/DirichletReg.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘glmnet’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘glmnet’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘DivMelt-Ex.R’ failed
The error most likely occurred in:

> ### Name: DivMelt_gui
> ### Title: User Interface for the Diversity Assay Analysis Tool
> ### Aliases: DivMelt_gui
> ### Keywords: interface
> 
> ### ** Examples
> 
> ##
> library (DivMelt)
> DivMelt_gui()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DivMelt_gui ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs   4.2Mb
Running examples in ‘dpa-Ex.R’ failed
The error most likely occurred in:

> ### Name: dpa-package
> ### Title: Dynamic Path Approach for Analyzing time-dependent simulation
> ###   data
> ### Aliases: dpa-package dpa
> 
> ### ** Examples
> 
> #Start the GUI with:
> dpa.start()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dpa.start ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  17.8Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/dprep.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 352 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'DSL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 ...<ce><fc><fc><bc><e3>8X^^W<c6>X<bb><dd>^^F<fd><9a><a6><e1>E<ac>:^^O8<e7><e3><e9><de>><a1>^^_\^^G
                                                  <8e><ee>^^?<dc>q^^F<c7>1<c8>3^^L^^C<cc><c1>O<a9>3<fb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <fa><e8><de>e)<e9><8d><c6>_[<f7><86>^^]<97><e4><9d>^^@0<ad><bd><d7>}7<f2><fe><8c>p<b6>e\<d3>
                                        4<d3><e9><b4>i<9a>H<c0>^^A8<92><f9><f9>y<d3>4www<9f>>}<fa><f9>矟<d1>^^D.-<e7>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
\GenericError  ...                                
                                                    #4  \errhelp \@err@     ...
l.25 ...^^X^^R^^@<c6>&<9b>ͦ<d3><e9>l<d6>L<a7><e3><a6>Yo6<9f><ee><ec><<e7>|<ab>Ri
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because DT.Rmd appears to be an R Markdown v2 document.
Quitting from lines 23-25 (DT.Rmd) 
Error: processing vignette 'DT.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   3.6Mb
Error in re-building vignettes:
  ...
  input string 371 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 387 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dtw.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...4?<fa><e8><a3>w<de>y<87><88>T^^?)<e5><ec><ec>,<98><8f><c7><e3>[[[<bf><fc><f2>˗_~)<84>x>^^C<ed>^
                                                  <e8><c1><83>^^G<fb>Z<ee>޽[<af><d7>{<9a>$<<e4><d9>	{<dd><c9><e1>^...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.15 ...<bf><93>^^?<a1><f6><b1> z><93>^^O<b4><fb><c1><88><cb>KW<9c><bd><93><8a><96><a3>^^P<84><87>^^P²<ac>\.<f7>
                                                  <e8>ѣ^^O><f8> <97>˽<fa>꫻<bb><bb><b3><b3><b3>g<b7><f4><bb>...
! You can't use `\spacefactor' in math mode.
\add@accen
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘ggm’ ‘tcltk’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘ggm’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘dynamicGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: DynamicGraph
> ### Title: DEPRECATED: Simple interface to dynamicGraph
> ### Aliases: DynamicGraph
> ### Keywords: dplot hplot iplot dynamic graphs methods multivariate
> 
> ### ** Examples
> 
> require(tcltk); require(dynamicGraph)
> 
> # Example 1:
> 
> W <- dg(as(new("dg.simple.graph", vertex.names = 1:5), "dg.graph"),
+         control = dg.control(title = "Very simple"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: dg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.2Mb
    libs  15.2Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs     2.4Mb
    models   4.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Eagle.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/easyDes.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eechidna.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eegkit.Rcheck/00install.out’ for details.
installed size is 42.5Mb
  sub-directories of 1Mb or more:
    libs  42.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EKMCMC.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 421 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'elrm.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.20 ...V^^AZ^^[<e1>dF^^L{^^C<94>ұ<b1><b1>`0<88><a4>^^[<86>Q<ab>հj<92><c9>d<ae>\<b9>
                                                  ^^B^^@mm<da>^^^<bb>r<a2>f樺ǈ;<cd>4<a7>s...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.25 <c1><8e>N<92>$<d4>:<8c>^^A<d8>^^X<8e><e3>J<a5>R<8b>^^[ ^^G><bd>c,^^Y<9d>B<f5><a9>}
                                             !<d0>^^Y<f8><ec>	<97>𥪪<f5>z<9d><b5><cb>^^Y<d1>X>d<87><8f>u{t!...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.45 x<9c><ed>\<cf>
          k^^[<d7>^^V>Q쪢<89
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘hgu133plus2.db’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EMCC.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs  16.8Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  20: set_TextType(methods_file)
  21: to_docbook(file)
  22: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  23: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 76 SKIPPED: 5 FAILED: 2
  1. Error: We return TRUE when validating a valid just created eml object with latin1 encoding (@test-validation.R#75) 
  2. Error: We return TRUE when validating a valid just created eml object (@test-validation.R#89) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/emma.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘clusterSim’ ‘earth’
  Please remove these calls from your code.
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
Packages in Depends field not imported from:
  ‘clusterSim’ ‘earth’
  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$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
'showtext.begin()' is now renamed to 'showtext_begin()'
The old version still works, but consider using the new function in future code
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 46-54 (phylomoji.Rmd) 
Error: processing vignette 'phylomoji.Rmd' failed with diagnostics:
object 'clado.build' not found
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘FactoMineR’ ‘MASS’ ‘Rcmdr’ ‘SensoMineR’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Namespace in Imports field not imported from: ‘BiocParallel’
  All declared Imports should be used.
Missing or unexported object: ‘xcms::profMat’
Error in re-building vignettes:
  ...
Warning 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]="./webshotf28074b1d313.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf28074b1d313.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/episensr.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions: ‘methods’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/epitable.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...<e5><81>h	ԂXqI<a9><c9><c0>H^^H<b5>N<93>K<c6>C<99><e0>^^D_i<aa>:<d3>&<96><df><e2><d7>9<dc><e7>/}
                                                  <c4>v,Gg!<c6>wν<ba><e7><9e><df>=<f7>|\ydkk<8b>N.<8d>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.15 ...<99><e0>^^D_i<aa>:<d3>&<96><df><
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: Argument mod1 is deprecated; please use mods and which instead. 
2: Argument mod2 is deprecated; please use mods and which instead. 
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 390 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 391 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 405 is invalid in this locale
6: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 406 is invalid in this locale
7: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Execution halted
Running examples in ‘erpR-Ex.R’ failed
The error most likely occurred in:

> ### Name: erp.infl
> ### Title: inspect the influence of a subject on the average (single
> ###   electrode).
> ### Aliases: erp.infl
> 
> ### ** Examples
> 
> 
> data(ERPsets)
> 
> erp.infl(base="Exp1_word_subj", numbers=1:20, electrode="OZ", 
+ startmsec=-200, endmsec=1500, erplist=ERPsets)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: erp.infl ... handshake -> fun -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ess.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/estprod.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘SNPRelate’ ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/eventstudies.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/EventStudy.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Evomorph.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Loading required package: TH.data
Loading required package: MASS

Attaching package: 'TH.data'

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

    geyser

Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'evtree.tex' failed.
LaTeX errors:
! TeX capacity exceeded, sorry [text input levels=15].
\@filef@und ->evtree.tpt 
                         
l.16 ...BO=<b5><e4><d0><de>r<88><ce>m)<88>B<f1><a1><a5>X^^Em^^E)^^NYX-&<c4>M<bd>x-<8c><9e>\[
                                                  <d3><dd>纛<84>H<ef><f0><a9><e7><ed>S^^\<fd><b0>c'<ca><d3><f7> vg...
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'exams.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...^^^{<ec><bd><e7>Rȭ<f4>蛡<85>P^^]bL^^L6^^L<ac>^^W<e1><d6>-^^Y<b4>Y\U
                                                  <e2><8f>ǻU<ed><8d><f3>K<fa>^^O_<f5><fe><ad>^^Sےc'<91><ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>RQJY<96>5`'A^^P<ec><ef><ef><97><cb><e5>z<bd>n<9a>&<fa>!<a2><ad><ad><ad><d9><d9>Y4^^[<b0><b7><b8>\q
                                                  <e6>|Ypb<8e>a<ba>D"<81><89>'<a2>z<bd><de><ed>v<cf>1<df>^^W+...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Please use \mathaccent for accents in math mode.
\add@accent ...@sp
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘expands-Ex.R’ failed
The error most likely occurred in:

> ### Name: cellfrequency_pdf
> ### Title: Computes the probability distribution of cellular frequencies
> ###   for a single mutation.
> ### Aliases: cellfrequency_pdf
> 
> ### ** Examples
> 
> freq=seq(0.1,1.0,by=0.01);
> cfd=cellfrequency_pdf(af=0.26,cnv=1.95,pnb=0,freq=freq, max_PM=6)
Error in .jcall("core.utils.Common", "V", "setALLOWED_FREQUENCIES", .jarray(as.double(freq))) : 
  RcallMethod: cannot determine object class
Calls: cellfrequency_pdf -> .jcall -> .External
Execution halted
Errors in running code in vignettes:
when running code in ‘expands.Rnw’
  ...
+     all))

> SPs = clusterCellFrequencies(cfd$densities[toUseIdx, 
+     ], precision)
[1] "Clustering  0 probability distributions..."
[1] "Clustering agglomeration method: average"

  When sourcing ‘expands.R’:
Error: object must be a numeric matrix
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'expands.Rnw' failed with diagnostics:
 chunk 5 
Error in .local(object, ...) : object must be a numeric matrix

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/factoptd.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/famSKATRC.Rcheck/00install.out’ for details.
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  9: value[[3L]](cond)
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, handled)
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_quick.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  12.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.1Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  14.6Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.8Mb
Missing or unexported objects:
  ‘destiny::DPT’ ‘destiny::random_root’
Running examples in ‘FateID-Ex.R’ failed
The error most likely occurred in:

> ### Name: dptTraj
> ### Title: Inferenence of diffusion pseudotime (DPT) for all cells on a
> ###   differentiation trajectory
> ### Aliases: dptTraj
> 
> ### ** Examples
> 
> 
> x <- intestine$x
> y <- intestine$y
> tar <- c(6,9,13)
> fb <- fateBias(x,y,tar,z=NULL,minnr=5,minnrh=10,nbfactor=5,use.dist=FALSE,seed=NULL,nbtree=NULL)
randomforest 1 15 
randomforest 2 15 
randomforest 3 14 
randomforest 4 13 
randomforest 5 15 
randomforest 6 15 
randomforest 7 13 
randomforest 8 14 
randomforest 9 13 
randomforest 10 13 
randomforest 11 14 
randomforest 12 14 
randomforest 13 15 
randomforest 14 15 
randomforest 15 14 
randomforest 16 13 
randomforest 17 10 
randomforest 18 5 
> dr <- compdr(x,z=NULL,m="cmd",k=2,lle.n=30,dm.sigma=1000,dm.distance="euclidean",tsne.perplexity=30)
> trc <- dptTraj(x,y,fb,trthr=.25,distance="euclidean",sigma=1000)
Error: 'random_root' is not an exported object from 'namespace:destiny'
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 137-138 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
The sigma parameter needs to be NULL, numeric or a 'Sigmas' object, not a 'character'.
Execution halted
Running examples in ‘FCMapper-Ex.R’ failed
The error most likely occurred in:

> ### Name: graph.fcm
> ### Title: Fuzzy cognitive map graph
> ### Aliases: graph.fcm
> 
> ### ** Examples
> 
> 
> matrix = matrix(nrow=7,ncol=7)
> matrix[1,] = c(0,-0.5,0,0,1,0,1)
> matrix[2,] = c(1,0,1,0.2,0,0,0.6)
> matrix[3,] = c(0,1,0,0,0,0,0)
> matrix[4,] = c(0.6,0,0,1,0,0,0.1)
> matrix[5,] = c(0,0.5,0,0,1,0,-0.6) 
> matrix[6,] = c(0,0,-1,0,0,0,0)
> matrix[7,] = c(0,0,0,-0.5,0,0,1)
> concept.names = c("A","B","C","D","E","F","G")
> 
> results = nochanges.scenario(matrix,iter=25,concept.names)
> 
> graph.fcm(matrix,concept.sizes=results$Equilibrium_value,concept.names)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "font".
Calls: graph.fcm ... .tkplot.convert.font -> <Anonymous> -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
installed size is 39.0Mb
  sub-directories of 1Mb or more:
    libs  38.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fdaPDE.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   6.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fds.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyread.hmd: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  read.table
Consider adding
  importFrom("utils", "read.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/feature.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ 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: ‘tools’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘tools:::fetchRdDB’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keyparseHelp: no visible global function definition for ‘help’
parseHelp: no visible global function definition for ‘unzip’
Undefined global functions or variables:
  help unzip
Consider adding
  importFrom("utils", "help", "unzip")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/FieldSim.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyfieldsim: no visible global function definition for ‘rnorm’
midpoint: no visible global function definition for ‘rnorm’
setAtlas_under: no visible global function definition for ‘runif’
setCovf_under : Ibeta: no visible global function definition for
  ‘pbeta’
visualize: no visible global function definition for ‘colorRampPalette’
Undefined global functions or variables:
  colorRampPalette pbeta rnorm runif
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("stats", "pbeta", "rnorm", "runif")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-87 (fiftystater.Rmd) 
Error: processing vignette 'fiftystater.Rmd' failed with diagnostics:
ScaleColorPlane was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because Best_Prectices.Rmd appears to be an R Markdown v2 document.
Quitting from lines 2-23 (Best_Prectices.Rmd) 
Error: processing vignette 'Best_Prectices.Rmd' failed with diagnostics:
could not find function "doc_date"
Execution halted
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘methods’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘fisheyeR-Ex.R’ failed
The error most likely occurred in:

> ### Name: POIcoords<-
> ### Title: Update POI slots
> ### Aliases: POIcoords<-
> 
> ### ** Examples
> 
>    ## IRIS Example
>    data(iris)
>    
>    # distance of each element to each dimension max and min
>    matrizSim = cbind(
+                1 - (max(iris[,1]) - iris[,1]) / (max(max(iris[,1]) - iris[,1])),
+                1 - (max(iris[,2]) - iris[,2]) / (max(max(iris[,2]) - iris[,2])),
+                1 - (max(iris[,3]) - iris[,3]) / (max(max(iris[,3]) - iris[,3])),
+                1 - (max(iris[,4]) - iris[,4]) / (max(max(iris[,4]) - iris[,4])),
+ 
+                1 - (min(iris[,1]) - iris[,1]) / (min(min(iris[,1]) - iris[,1])),
+                1 - (min(iris[,2]) - iris[,2]) / (min(min(iris[,2]) - iris[,2])),
+                1 - (min(iris[,3]) - iris[,3]) / (min(min(iris[,3]) - iris[,3])),
+                1 - (min(iris[,4]) - iris[,4]) / (min(min(iris[,4]) - iris[,4])))
> 
>    # exaggerate diffs
>    matrizSim  = matrizSim^3 
>    
>    # Create POI plot
>    irisPOI = POICreate('POI')
>    irisPOI@matrizSim <- matrizSim
>    irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
+                              'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')
>    POIcoords(irisPOI) <- POICalc(irisPOI ,length(irisPOI@wordsInQuery))
>    irisPOI@docs <- cbind(matrix(seq(1:nrow(irisPOI@objeto))),matrix(seq(1:nrow(irisPOI@objeto))))
>    irisPOI@colores <- c(rep(2,50),rep(3,50),rep(4,50))
>    try(rm('POI.env'), silent = T)
Warning in rm("POI.env") : object 'POI.env' not found
>    plotPOI(irisPOI)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: plotPOI ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fit4NM.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/flatr.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
     estimating mean dists
     estimating probs of migration
     estimating median dists
     creating output DONE!
  DONE!
  bird likely did not move, exiting without result
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 27 SKIPPED: 0 FAILED: 2
  1. Error: map_flightr_ggmap_works (@test_data_result_summary_and_plotting.R#36) 
  2. Error: plot_util_distr_works (@test_data_result_summary_and_plotting.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Codoc mismatches from documentation object 'c':
\S4method{c}{float32}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/foodweb.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Error in re-building vignettes:
  ...
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Warning in private$.dnames[[1]][rows] = rownames(data) :
  number of items to replace is not a multiple of replacement length
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ClassDiagram.tex' failed.
LaTeX errors:
! Package pgfkeys Error: I do not know the key '/forest/package@options/linguis
tics' and I am going to ignore it. Perhaps you misspelled it.

See the pgfkeys package documentation for explanation.
Type  H <return>  for immediate help.
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ForImp.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyForImp: no visible global function definition for ‘head’
ForImp: no visible global function definition for ‘tail’
ForImp: no visible global function definition for ‘dist’
medianimp: no visible global function definition for ‘quantile’
rancatmat: no visible global function definition for ‘runif’
transfmatcat: no visible global function definition for ‘qnorm’
transfmatcat: no visible global function definition for ‘sd’
Undefined global functions or variables:
  dist head qnorm quantile runif sd tail
Consider adding
  importFrom("stats", "dist", "qnorm", "quantile", "runif", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because formattable-data-frame.Rmd appears to be an R Markdown v2 document.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
  input string 346 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Formula.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.22 p<81>'<f6>^^\<f3>`<cc><e9><e7><c0>^^Sa<ee>yB<b0><81><c4>q<9c><fe>7<f2><e7><8a>9/<db><de><fc><b4>\<f1>
                                           <fd>ޫ<9d><c6>E<80><82><f4>^^V<e7>^^\<b8>^^G^^Y0<c6>hG^^W<87><cc>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.23 ...G<9e>3<97><cb><cd><cc><cc><d4>j5<ac><93>B<a1><b0><b0><b0>P(^^T^^R<89><84>a^^X<aa><aa>nmm)<8a><e2>y^
                                                  <a5>Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>...
! Undefined control sequence.
l.23 ...Ra<8c>U*^^U^^\<c3>i<b7><db><c8>|2<c6><f0><ab>^^P<e2>ѣG<b3><b3><b3>B<88>X,<96><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/formulize.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frequencies.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/frontiles.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyROCscore: no visible global function definition for ‘par’
ROCscore: no visible global function definition for ‘axis’
ROCscore: no visible global function definition for ‘mtext’
ROCscore: no visible global function definition for ‘legend’
alphafrontier.2d: no visible global function definition for ‘par’
alphafrontier.2d: no visible global function definition for ‘polygon’
alphafrontier.2d: no visible global function definition for ‘lines’
alphafrontier.2d: no visible global function definition for ‘points’
alphafrontier.3d: no visible global function definition for ‘layout’
alphafrontier.3d: no visible global function definition for ‘barplot’
alphafrontier.3d: no visible global function definition for ‘axis’
alphafrontier.3d: no visible global function definition for ‘lines’
alphafrontier.3d: no visible global function definition for ‘na.omit’
ordermfrontier.2d: no visible global function definition for ‘par’
ordermfrontier.2d: no visible global function definition for ‘polygon’
ordermfrontier.2d: no visible global function definition for ‘lines’
ordermfrontier.2d: no visible global function definition for ‘points’
ordermscore.boot: no visible global function definition for ‘sd’
Undefined global functions or variables:
  axis barplot layout legend lines mtext na.omit par points polygon sd
Consider adding
  importFrom("graphics", "axis", "barplot", "layout", "legend", "lines",
             "mtext", "par", "points", "polygon")
  importFrom("stats", "na.omit", "sd")
to your NAMESPACE file.
Running examples in ‘FSelector-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.simple.formula
> ### Title: Converting to formulas
> ### Aliases: as.simple.formula
> 
> ### ** Examples
> 
>   data(iris)
>   result <- cfs(Species ~ ., iris)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: cfs ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.0Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, handled)
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 32 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-discretize.R#20) 
  2. Error: (unknown) (@test-information_gain.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fso.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ftsa.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fullfact.Rcheck/00install.out’ for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/fusionclust.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 191 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 192 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 200 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'CNY.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.31 ...<f9><f3><a7>\.;q*<e0><88><ed><ed><ed><d0> <ac>~<d0><e6>+W<88><ca><e5>2J<fb>Μ^^@σ<83><83>0<89><f1>x\T
                                                  <c3>^^Q^^Y<e2>~^^H<ed><de>^^U`<8c><f5><f7><f7><e3><93>s<ce>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.34 ΘeY<b9>\N
            <84>x<a2>B^^DX^^@E?T<ed>^^P<91>E<a3>ю<8e><8e>|>/<8a>GD<94><cb>尙<c3><dd>z^^E<f6>^^P+x<^^^I<92>$I<d2>4M<92>$UU^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.36 <8c>C@^^OP^^D\<b2>
                 <c0><fd>\<a6>A<bb>X<ee><a0><cd>7x<8d><a1><f2><d9>ù<87>	<99><9e><9e>~<f4><e8>^^QB<8d><ab>W<af>^^B^^Tt^<f2><a2>]^^Nq<d2>^^@<d4>#O<ab>^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you h
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages required and available but unsuitable versions:
  ‘grDevices’ ‘graphics’ ‘stats’

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

> ### Name: demoDist
> ### Title: Interface for demonstrating the gamlss.family distributions
> ### Aliases: demoDist
> ### Keywords: distribution regression
> 
> ### ** Examples
> 
> ## do not run 
> demoDist()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: demoDist ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'jss.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.18 <92><a1>><df><ef><af>NJ^^C^^C~<d2><e7>^^[^^Zhl|<fb><f6><ed><e6><a3>ٶ}
                                       <f3><e6>M۶gffZ<b6>ll<86><bd><f6><80>^^V<dc>;^^W<f2><e9>k<f5>X<ea>w<9f><fc><e5><ef>֦...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Undefined control sequence.
l.18 ...`<8c>QJ3<99>L^^?^^?<ff><e0><e0> ^^@PJ^^S<89>D:<9d>ƨ<ea><ec>ٳ<8b><8b><8b>W<ae>\<99>
                                                  <9e><9e><be>r<e5><ca><de>'<b7><b7>@<e3><87>a<cb>^^^b<96><e6>]fff^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
        
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   9.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gastempt.Rcheck/00install.out’ for details.
installed size is 59.4Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     56.5Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gdimap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GD.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/genBaRcode.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/geoelectrics.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/geoops.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key.ldots.set: no visible global function definition for ‘getS3method’
grf: no visible global function definition for ‘chull’
image.grf: no visible global function definition for ‘heat.colors’
image.krige.bayes: no visible global function definition for
  ‘heat.colors’
legend.krige: no visible global function definition for ‘heat.colors’
points.geodata: no visible global function definition for
  ‘terrain.colors’
points.geodata: no visible global function definition for ‘gray’
read.geodata: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  chull getS3method gray heat.colors read.table terrain.colors
Consider adding
  importFrom("grDevices", "chull", "gray", "heat.colors",
             "terrain.colors")
  importFrom("utils", "getS3method", "read.table")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 59-70 (gitrd-vignette-introduction.Rmd) 
Error: processing vignette 'gitrd-vignette-introduction.Rmd' failed with diagnostics:
replacement has 0 rows, data has 54
Execution halted
Package which this enhances but not available for checking: ‘stable’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 102-115 (examples-from-paper.Rmd) 
Error: processing vignette 'examples-from-paper.Rmd' failed with diagnostics:
StatEdges was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ggdmc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GGEBiplotGUI.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘nipals’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc05e7bb77beb.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc05e7bb77beb.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because using_ggmcmc.Rmd appears to be an R Markdown v2 document.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: tidyr
Loading required package: ggplot2
Registering fonts with R
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ggpmisc.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 40.1Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'glmertree.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Oh
           ^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 x<9c><ed>\Oh^^S<dd>^^V?6<af>h<a4>d<de><c5>"!<90><a6>\<f0>
                                I<bf>/<84>@PP(qQ<9e><bb>"HPą^^[<83> .<ba><ea>օ.\(.<ec>f<b6><fe>A^^H<b8><c8><e2>[<d8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<95>R<9a><a6>y<f7><ee>]<ce><f9><f5><eb><d7>oܸa^^X^^F<be>^^B<df>^^E^^@x<81><d7>8!<e7>\<d3>
                                                  <b4>T^^]<8d><96><be><b6>3LOO^^?<fd><fa>u'O<bd>y<f3>f<87>...
The control sequence at the end of the top line
of your error message was never 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running the tests in ‘tests/bym.R’ failed.
Last 13 lines of output:
  + 
  + kentucky = mergeBugsData(kentucky, kSummary)
  + 
  + if(require('sp', quietly=TRUE)) {
  +   pdf("spplotBym.pdf",height=4,width=8)
  +   print(spplot(kentucky, "FittedRateCounty.mean"))
  +   dev.off()
  + }
  + 
  + }
  Error in R2OpenBUGS::bugs(forBugs$ragged, inits = int2, model.file = "bym.txt",  : 
    Cannot find the OpenBUGS program
  Execution halted
installed size is 49.3Mb
  sub-directories of 1Mb or more:
    libs  48.6Mb
installed size is 57.2Mb
  sub-directories of 1Mb or more:
    libs  56.1Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: htmlTable
  ── 1. Error: (unknown) (@test-fig_caption.R#6)  ────────────────────────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(fn, output_file = file.path(td, "tmp.html")) at testthat/test-fig_caption.R:6
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 311 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-fig_caption.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GMSE.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/googlePolylines.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 205 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 206 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 214 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'googleVis.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <ed><c1>E<98>e҃<a7>z<ea>ѣ<82>x^^V<(xt^^?<80><88><ee>\E
                                  <8a>B^^[<88>^^Y<e2><L'a"A:'^^AM<b2><c9>V<fb><98>&Vs<b0><f9>^^\^^^^^\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<97><cb>=x<f0>`vv<f6>ڵk<87>^^O^^_<be>x<f1><a2>i<9a><8f>^^_?<f6>}<ff>ʕ+^^W.\<98>
                                                  <9d><9d><d5>4mmmM<92><a4><b9><b9><b9>;w<ee>D^^^<d5>n<b6>[<d3>4...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ^^@^^X<86>^^A^^@<c5>b<b1><eb> {<ba><9f><84><90>r<b9>L<bb>\<b3>
                                  <d9>$<84><8c><8f><8f>˲L^^Hy<f9><f2><a5><e7>y<93><93><93><8d>F^^C^^@<c2>0ܖ<a4>q^^O
The control sequence at the end of the top line
of your error message was nev
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPC.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/II_PreProcessing.R':
invalid multibyte character in parser at line 59
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GPoM.Rcheck/GPoM/doc/IV_VisualizeOutputs.R':
invalid multibyte character in parser at line 30
installed size is 54.0Mb
  sub-directories of 1Mb or more:
    libs  51.7Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1. Error: CPU vclMatrix integer scalar initializers (@test_cpu_vclMatrix_classes.R#148) 
  2. Failure: gpuVector Single Precision Element-Wise Logs (@test_gpuVector_math.R#140) 
  3. Error: Non-Shared memory between vclMatrix & vclVector (@test_shared_memory.R#53) 
  4. Error: Switching GPUs vclMatrix Double Precision Matrix Multiplication (@test_switch_gpu_vclMatrix_algebra.R#480) 
  5. Error: Switching GPUs vclMatrix Double Precision Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#507) 
  6. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#535) 
  7. Error: Switching GPUs vclMatrix Double Precision Unary Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#567) 
  8. Error: Switching GPUs vclMatrix Double Precision Matrix Addition (@test_switch_gpu_vclMatrix_algebra.R#593) 
  9. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Addition (@test_switch_gpu_vclMatrix_algebra.R#621) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R   5.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GrammR.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/groupsubsetselection.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/GUTS.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘gWidgets.Rnw’
  ...

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


  When sourcing ‘gWidgets.R’:
Error: [tcl] invalid command name "toplevel".
Execution halted
Error in re-building vignettes:
  ...
Loading required package: gWidgetstcltk
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Loading required package: digest
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".

Loading required package: gWidgetstcltk
Error : .onAttach failed in attachNamespace() for 'gWidgetstcltk', details:
  call: structure(.External(.C_dotTcl, ...), class = "tclObj")
  error: [tcl] invalid command name "option".


Error: processing vignette 'gWidgets.Rnw' failed with diagnostics:
 chunk 3 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".

Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/gWidgetstcltk.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/h5.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/happybiRthday.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘ggtree’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hdf5r.Rcheck/00install.out’ for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/heims.Rcheck/00install.out’ for details.
Running examples in ‘helixvis-Ex.R’ failed
The error most likely occurred in:

> ### Name: draw_wenxiang
> ### Title: Create wenxiang diagrams to visualize alpha helical sequences.
> ### Aliases: draw_wenxiang
> 
> ### ** Examples
> 
> draw_wenxiang("TestWenxiang", "AREKHLVLLKREGDIWKL")
Error in rJava::.jnew("Sequence") : 
  java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
Calls: draw_wenxiang -> <Anonymous> -> .External
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 146-147 (Visualization.Rmd) 
Error: processing vignette 'Visualization.Rmd' failed with diagnostics:
java.lang.UnsupportedClassVersionError: Sequence : Unsupported major.minor version 52.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hgam.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘grplasso’ ‘lattice’ ‘rgl’ ‘splines’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘HIBPwned-Ex.R’ failed
The error most likely occurred in:

> ### Name: account_breaches
> ### Title: Search for data breaches associated with one or more accounts.
> ### Aliases: account_breaches
> 
> ### ** Examples
> 
> account_breaches(c("steff.sullivan@gmail.com","stephanie.g.locke@gmail.com"))
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: Invalid certificate chain
Calls: account_breaches ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 31 SKIPPED: 0 FAILED: 7
  1. Error: account_breaches works for a single account (@test-account_breaches.R#8) 
  2. Error: account_breaches works for multiple accounts (@test-account_breaches.R#54) 
  3. Error: breached_site works (@test-breached_site.R#6) 
  4. Error: breached_sites works (@test-breached_sites.R#6) 
  5. Error: data_classes works (@test-data_classes.R#4) 
  6. Error: pastes works for a single account (@test-pastes.R#8) 
  7. Error: pastes works for multiple accounts (@test-pastes.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 23-24 (HIBP.Rmd) 
Error: processing vignette 'HIBP.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HiCblock.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HierO.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        7.8Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hiPOD.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPlotOptPower: no visible global function definition for ‘bmp’
PlotOptPower: no visible global function definition for
  ‘filled.contour’
PlotOptPower: no visible global function definition for ‘title’
PlotOptPower: no visible global function definition for ‘grey.colors’
PlotOptPower: no visible global function definition for ‘axis’
PlotOptPower: no visible global function definition for ‘polygon’
PlotOptPower: no visible global function definition for ‘legend’
PlotOptPower: no visible global function definition for ‘mtext’
PlotOptPower: no visible global function definition for ‘dev.off’
PlotOptPower: no visible global function definition for
  ‘terrain.colors’
ShowOptDesign: no visible global function definition for ‘head’
diffVariantError: no visible global function definition for ‘pbinom’
predictPoolNCP: no visible global function definition for ‘data’
probDetEqual3: no visible global function definition for ‘dbinom’
probDetEqual3: no visible global function definition for ‘pbinom’
Undefined global functions or variables:
  axis bmp data dbinom dev.off filled.contour grey.colors head legend
  mtext pbinom polygon terrain.colors title
Consider adding
  importFrom("grDevices", "bmp", "dev.off", "grey.colors",
             "terrain.colors")
  importFrom("graphics", "axis", "filled.contour", "legend", "mtext",
             "polygon", "title")
  importFrom("stats", "dbinom", "pbinom")
  importFrom("utils", "data", "head")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hoardeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/homals.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HomoPolymer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HRM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/hsdar.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘phyloseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
    doc    1.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-97 (api-packages.Rmd) 
Error: processing vignette 'api-packages.Rmd' failed with diagnostics:
Failed connect to api.github.com:443; Operation now in progress
Execution halted
Found the following significant warnings:
  Warning: multiple methods tables found for ‘colMeans’
  Warning: multiple methods tables found for ‘colSums’
  Warning: multiple methods tables found for ‘rowMeans’
  Warning: multiple methods tables found for ‘rowSums’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/humarray.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HUM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyCalculate3D: no visible global function definition for ‘persp’
CalculateHUM_Ex: no visible global function definition for ‘combn’
CalculateHUM_Plot: no visible global function definition for ‘plot’
CalculateHUM_Plot: no visible global function definition for ‘polygon’
CalculateHUM_Plot: no visible global function definition for ‘text’
CalculateHUM_Plot: no visible global function definition for ‘points’
CalculateHUM_Plot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  combn lines persp plot points polygon text
Consider adding
  importFrom("graphics", "lines", "persp", "plot", "points", "polygon",
             "text")
  importFrom("utils", "combn")
to your NAMESPACE file.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    dict   1.3Mb
    libs   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
trying URL 'https://arxiv.org/e-print/1406.4806v1'
Content type 'unknown' length 29273 bytes (28 KB)
==================================================
downloaded 28 KB

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HURDAT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/HybridFS.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘utils’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/iBUGS.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tcltk’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    2.1Mb
    libs   1.1Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.5Mb
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'ICS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1><bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...^S<df>^^V?ԇ<bc><89><a4>ÄMCRhnbta<a0>d6Ƙ<94>^^Ekw<fe>]<eb><c2>tk\<c1>
                                                  <bf>Ѕ1q<c9>ưe^^VT^^S^^S<88>^^S<a7><8d>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <c3>^^PB\<be>
            |<f9>Ǐ^^_<86>a<80>H!D&<93>A7|^^Z<86>a<9a>&c<8c>1<b6><b9><b9>9::jYV&<93>i<e3>z^^O<e0>իWM-+++{{{<bd>X<eb>d^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 cB<88><ef><9e>^^W<c4><e3>Q<c6>^^L<c7><f9>O2^^Yk^^
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  23.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/idmTPreg.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ifa.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  14.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ijtiff.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ilc.Rcheck/00install.out’ for details.
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       4.9Mb
    include   2.8Mb
    libs     18.6Mb
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

> ### Name: doIMRMC
> ### Title: MRMC analysis of the area under the ROC curve
> ### Aliases: doIMRMC
> 
> ### ** Examples
> 
> # Create a sample configuration file
> config <- sim.gRoeMetz.config()
> # Simulate an MRMC ROC data set
> dFrame.imrmc <- sim.gRoeMetz(config)
> # Analyze the MRMC ROC data
> result <- doIMRMC(dFrame.imrmc)
Warning in file(file, "rt") :
  cannot open file '/tmp/RtmpXL5nIG/imrmcDir/AUCperReader.csv': No such file or directory
Error in file(file, "rt") : cannot open the connection
Calls: doIMRMC -> <Anonymous> -> read.table -> file
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.03198493            0.03198493            0.12793972 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 11 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#26) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/incR.Rcheck/00install.out’ for details.
Running examples in ‘infer-Ex.R’ failed
The error most likely occurred in:

> ### Name: hypothesize
> ### Title: Declare a null hypothesis
> ### Aliases: hypothesize
> 
> ### ** Examples
> 
> # One binary variable
>   mtcars %>%
+     dplyr::mutate(am = factor(am)) %>%
+     specify(response = am, success = "1") %>%
+     hypothesize(null = "point", p = 0.75) %>%
+     generate(reps = 100, type = "simulate") %>%
+     calculate(stat = "prop")
Error in .subset2(x, i, exact = exact) : invalid subscript type 'symbol'
Calls: %>% ... [[.tbl_df -> NextMethod -> [[.data.frame -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 92-105 (flights_examples.Rmd) 
Error: processing vignette 'flights_examples.Rmd' failed with diagnostics:
invalid subscript type 'symbol'
Execution halted
Running examples in ‘Inflation-Ex.R’ failed
The error most likely occurred in:

> ### Name: INFL.core_tf
> ### Title: Computes the triple filter core inflation
> ### Aliases: INFL.core_tf
> ### Keywords: core filter triple
> 
> ### ** Examples
> 
> ipca <- ipca_sub
> INFL.core_tf(subits.var=ipca$ipca_ts, weights = ipca$weights_ts)
sh: line 1: 85685 Trace/BPT trap: 5       /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/x13ashtml /tmp/Rtmp11HgzC/x1314eb27fe7a814/iofile -n -s 2> /dev/null
Warning: running command '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/x13ashtml /tmp/Rtmp11HgzC/x1314eb27fe7a814/iofile -n -s 2>/dev/null' had status 133
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/../lib/libgfortran.3.dylib
  Expected in: /usr/lib/libSystem.B.dylib

dyld: Symbol not found: _mkostemp
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/x13binary/bin/../lib/libgfortran.3.dylib
  Expected in: /usr/lib/libSystem.B.dylib


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x12df89579
#1  0x12df88945
#2  0x7fff9078d5a9
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/interactionTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/interfr.Rcheck/00install.out’ for details.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
Package required and available but unsuitable version: ‘libcoin’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   7.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/IQCC.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘rcdk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
  input string 443 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 451 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 452 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 460 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'isocir.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 ...<b6>m<cb><f6><81>^^?<c9>?<e5><cc>B^^H<<c4><ef><f0>؞p<b9><cb>~<a6>i~<f3><cd>7<bf><fc><f2><8b>i<9a><86>a\<bf>
                                                  ~]<d7>u<<b7>m<bb>P(<88>^^V<b2>٬a^^X<d8><df><f4><f4><f4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<fd><f6><db><fe><9b>xud^^Lݼy<b3>'a<d6>u]Q^^T<f9><a7>a^^X?<fd><f4><93><a2>(<f1>x\^^H
                                                  <f1><e5><97>_^<bb>vm~~~gg<e7><d7>_^^?<9d><9d><9d>5^^L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<e6>y<fe><fc>y2<99><f4></<99>L<86><a3>^^E^^L,<95>J<9f>^^?<fe><b9><e3>8<99>L<e6>,<c8><eb>^^W\p
                                                  <dd>^^[<90><d7><cf>8<96><e5>4MS<d7>u<c6><d8><c2><c2><c2><d8><d
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
l.19 ...	]<d7>^^AJ^^R<89>D<b3>ٔ<f3><ef><ef><ef>g<b3><d9>J<a5><92><cd>f^^AP8<e7><e5><b2>_(d\^^W
                                                  <97>})<f6>^^@<ca>)D<84>^^_<be><bf><f3><d3>O<8d>7ޘ<e6><fc>2...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.24 <9e>^^P<91>g}}
             ^^]<d8>^^_^^A<8d><88>^^TEY^^<ae><d5>j<e8>^^Z<db><dc><dc>l6<9b>2<b7>B
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or
Calls: buildVignettes -> texi2pdf -> texi2dvi
In addition: Warning messages:
1: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 424 is invalid in this locale
2: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 425 is invalid in this locale
3: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 433 is invalid in this locale
4: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 434 is invalid in this locale
5: In grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 442 is invalid in this locale
Execution halted
Running the tests in ‘tests/test.R’ failed.
Last 13 lines of output:
  > testMD <- issuesData2md()
  > 
  > # Use default data to generate PDF
  > issuesGenPDF(style = "tint",
  +              RmdLocation =  system.file("rmarkdown/templates/", "tint.Rmd",
  +                                         package = "issueReporter"),
  +              outputFile = tempfile(pattern="ir", fileext=".pdf"),
  +              outputDir = tempdir(),
  +              md = testMD,
  +              setTitle = "Example Notes",
  +              setAuthor = "Author Name")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
Error in re-building vignettes:
  ...
Warning 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 52-55 (inspect.Rmd) 
Error: processing vignette 'inspect.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
Execution halted
Error in re-building vignettes:
  ...
 1: .Call(rmd_b64encode_data, readBin(inFile, "raw", n = fileSize))
 2: paste("data:", mime::guess_type(inFile), ";base64,", .Call(rmd_b64encode_data,     readBin(inFile, "raw", n = fileSize)), sep = "")
 3: .b64EncodeFile(inFile)
 4: sub(src, .b64EncodeFile(inFile), imgSrc, fixed = TRUE)
 5: FUN(X[[i]], ...)
 6: lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc)
 7: unlist(lapply(regmatches(html, m)[[1]], .b64EncodeImgSrc))
 8: .b64EncodeImages(ret)
 9: eval(expr, envir, enclos)
10: eval(quote({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)}), new.env())
11: eval(expr, envir, enclos)
12: eval(expr, p)
13: eval.parent(substitute(eval(quote(expr), envir)))
14: local({    oldwd <- setwd(filedir)    on.exit(setwd(oldwd))    .b64EncodeImages(ret)})
15: markdown::markdownToHTML(out, output, encoding = encoding, ...)
16: knit2html(..., force_v1 = TRUE)
17: (if (grepl("\\.[Rr]md$", file)) knit2html_v1 else if (grepl("\\.[Rr]rst$",     file)) knit2pdf else knit)(file, encoding = encoding, quiet = quiet,     envir = globalenv())
18: vweave(...)
19: engine$weave(file, quiet = quiet, encoding = enc)
20: doTryCatch(return(expr), name, parentenv, handler)
21: tryCatchOne(expr, names, parentenv, handlers[[1L]])
22: tryCatchList(expr, classes, parentenv, handlers)
23: tryCatch({    engine$weave(file, quiet = quiet, encoding = enc)    setwd(startdir)    find_vignette_product(name, by = "weave", engine = engine)}, error = function(e) {    stop(gettextf("processing vignette '%s' failed with diagnostics:\n%s",         file, conditionMessage(e)), domain = NA, call. = FALSE)})
24: buildVignettes(dir = "/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Jdmbs.Rcheck/vign_test/Jdmbs")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/jdx.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/JumpTest.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/JuniperKernel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kader.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KappaGUI.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Error in re-building vignettes:
  ...
  input string 238 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 244 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'kernlab.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?<ec>dc'U<a5>^^N-.u<ba><b2><bb>E<b8><88>e<a3>V^^P<b0>!<dd>^^F<ab><84>^ғo=<e4><a4><d0>C^^O=<e5>VBo<f9>^^C^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...<f7>}^^Lb<9a>f<9c>5<9f><b8>~<fd>zL<f2><d6><d6><d6>^^XcCCC+++^^_|<f0><c1><fa><fa>z6<9b>}
                                                  <f0><e0><c1><e8><e8><a8><e7>yO<9e><<f1><<8f><88><d2><e9><f4><da><da><da>ŋ^^W...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.17 ...O<9e><<f1><<8f><88><d2><e9><f4><da><da
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/keyholder.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmcudaR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kml.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kmlShape.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    libs   3.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/komadown.Rcheck/00install.out’ for details.
Running examples in ‘kstIO-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_kbase
> ### Title: Read base file
> ### Aliases: read_kbase
> ### Keywords: file
> 
> ### ** Examples
> 
> # Produce a base file
> library(kst)
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
> data(DoignonFalmagne7)
> b <- kbase(kspace(kstructure(as.pattern(DoignonFalmagne7$K, as.set=TRUE))))
> write_kbase(b, "DF7.bas", "KST") # (Old) KST format
Error in write_kbase(b, "DF7.bas", "KST") : 
  “x” must be of class “kbase” or “matrix”!
Execution halted
Errors in running code in vignettes:
when running code in ‘kstIO.Rnw’
  ...

> write_kstructure(ksp, "DF7.struct")

> write_kspace(ksp, "DF7.space", format = "matrix")

> write_kbase(b, "DF7.bas", format = "KST")

  When sourcing ‘kstIO.R’:
Error: “x” must be of class “kbase” or “matrix”!
Execution halted
Error in re-building vignettes:
  ...
Attaching package: ‘stringr’

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

    %>%

Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 2 (label = write-functions) 
Error in write_kbase(b, "DF7.bas", format = "KST") : 
  “x” must be of class “kbase” or “matrix”!
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/kst.Rcheck/00install.out’ for details.
installed size is 16.0Mb
  sub-directories of 1Mb or more:
    libs          11.1Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/later.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! LaTeX Error: Unknown float option `H'.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                       
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LCAvarsel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LCox.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lctools.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ldat.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ldhmm.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/leafSTAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lfl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/libcoin.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/libstableR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lifecontingencies.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0curl: (7) Failed connect to localhost:54321; Connection refused
  [1] 7
  ── 1. Error: (unknown) (@test-h2o.R#4)  ────────────────────────────────────────
  H2O failed to start, stopping execution.
  1: h2o.init() at testthat/test-h2o.R:4
  2: stop("H2O failed to start, stopping execution.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-h2o.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘reactR’
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    doc        1.5Mb
    libs      21.9Mb
    testdata   1.5Mb
Error in re-building vignettes:
  ...
  input string 785 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'lmer.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Mh
           ^^TK^^P<ae><97>(q$<ee>؈!.L6^^L/($oYX^^Hx^^H<eb>!<a0>'o<de><<eb>ٓ^^A/<a2>O<f0>]ċ^^G<f5>^^]<84><e7>A...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...F<a0><ba>v<ed>Zggg<ad>V{<fd><fa>5^^Q9<8e>388866<a6><94><8a><e3>^^X<fd>^^]<c7><c1><83><ae>^
                                                  <bd><9a>J<a5>l<db>v^^\^^G<9f>J<a9><87>^^O^^_<c6>q|...
! Extra }, or forgotten $.
l.17 Ԓ<da>[}
          <b8>ӄ<f6><a0><9c>0^^L<89>(<9b><cd><e2>^^A<98><ce>0^^L<85>^^BOm<b9>\^^^^^Z^^Z<8a><a2><88><a7>?<9b><cd>"@a<ce>0<8e>eYP{<a1>P<c0>O<<c8><e3>...
I've deleted a group-closing 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in readLines(con) :
  incomplete final line found on 'localsolver.Rmd'
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because localsolver.Rmd appears to be an R Markdown v2 document.
sh: localsolver: command not found
Quitting from lines 66-68 (localsolver.Rmd) 
Error: processing vignette 'localsolver.Rmd' failed with diagnostics:
has.localsolver(ls.path) is not TRUE
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.mode.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘distr’
  All declared Imports should be used.
Package in Depends field not imported from: ‘logcondens’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/logcondens.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 442 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'logcondens.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.16 ...[<f8><f8>㏻~8<9d>NC^^\<cb>d2<ba><ae>^^SB><fd><f4>ӑ<91>^^Q!D&<93><f9>ꫯ<de>}
                                                  <f7><dd>vڙ<9d><9d><b5>,˲,<ce><f9><d7>_^^?=11^^Aa...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.23 ...<aa>mۚ<a6>I<bb>b<8c><fd><fa><eb><af><c8>e<99><aa><aa><c2>-If<c6>X4^^Z-<97>ˊ<a2>p<ce>UU<a5><94>z<bd>^
                                                  7<c9>^^O<91><a3><92><f3><f0><95><c1><be><bb><a7><bf><8c><e8>^^@^<a1>PP^...
! You can't use `\spacefactor' in math mode.
\@ ->\spacefactor 
                  \@m 
l.24 ...<aa><aa>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/longitudinalData.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/loon.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyTOS2D: no visible global function definition for ‘medpolish’
countTextures: no visible global function definition for ‘medpolish’
plot.imageQT: no visible global function definition for ‘segments’
simTexture: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  medpolish rnorm segments
Consider adding
  importFrom("graphics", "segments")
  importFrom("stats", "medpolish", "rnorm")
to your NAMESPACE file.
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  44.7Mb
Package required and available but unsuitable version: ‘partykit’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lumberjack.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/lwgeom.Rcheck/00install.out’ for details.
installed size is 24.3Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Maeswrap.Rcheck/00install.out’ for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  15.5Mb
objc[7063]: Class GNotificationCenterDelegate is implemented in both /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/magick.Rcheck/magick/libs/magick.so and /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rsvg/libs/rsvg.so. One of the two will be used. Which one is undefined.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/manet.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Warning in arrange_impl(.data, dots) :
  '.Random.seed' is not an integer vector but of type 'NULL', so ignored
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotcc924daff2c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotcc924daff2c.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs  10.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd9ac60a56041.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd9ac60a56041.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MANOVA.RM.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MARSS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘MARSS:::is.diagonal’
  See the note in ?`:::` about the use of this operator.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   5.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   5.0Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mbbefd.Rcheck/00install.out’ for details.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  11.5Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  24.4Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mdpeer.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   3.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   4.7Mb
Error in re-building vignettes:
  ...
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mefa.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 <f0>F<b6>9<dc> <9d>N˗<b9>\N
                  <b6>?<<af><9c><a5>)^^EZ<f4>^^X<d2><e9>t*<95><9a><99><99><91>k<d2>u]<ae><fb><97>_~<f9><f0><c3>^^O
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 Ðmt]<c7><ca>._<be>\<ab>
                 <d5>^^Xc<8c><b1><a9><a9><a9>t:
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...^^L^^Yc<ba><ae><e3>^^Fs^^R<b3>w-g'S^^SӒN<a7>Og^^]OBG\^^O
                                                  <ba><ca><d9><c9>t^^Z<b8>^^G<82><a7>w<e9>ҥH$R<a9>T<e2><f1><f8>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.27 ...]<e6>^^D<cf><d9>lvhh<c8>u]<c8><c4>u<dd>۷o<ef><ec><ec><c4>b<b1>L&S<af><d7>^^]<c7><e9><ef><ef><c
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Mega2R.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package required and available but unsuitable version: ‘mem’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘shadowtext’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/meme.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mem.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyworkspace_management : tellme: no visible global function definition
  for ‘file.edit’
workspace_management: no visible global function definition for
  ‘object.size’
Undefined global functions or variables:
  file.edit object.size
Consider adding
  importFrom("utils", "file.edit", "object.size")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MergeGUI.Rcheck/00install.out’ for details.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/metaforest.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘EBImage’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/metaheuristicOpt.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/meteoland.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetFns.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MetSizeR.Rcheck/00install.out’ for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  11.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MFHD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MicroStrategyR.Rcheck/00install.out’ for details.
Missing or unexported object: ‘tools::CRAN_package_db’
Running examples in ‘miniGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeWidgetCmd
> ### Title: R functions to build a GUI window
> ### Aliases: makeWidgetCmd
> ### Keywords: utilities misc
> 
> ### ** Examples
> 
>   require(tcltk)
>   ##
>   ##  a simple example
>   ## 
>   g <- function(a=1,b=rnorm) {cat("--g--");paste("g(a,b)=",a+b(a))}
>   h <- function(a=1,b=3,c=3) {cat("--h--");paste("h(a,b,c)=",a+b+c)}
>   ## create functions
>   gg <- makeWidgetCmd("Hay it is g !!",g,GRAB=FALSE)
>   hh <- makeWidgetCmd("Hay h here !!",h,GRAB=FALSE)
>   ## calling them
>   gg()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: gg ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.8Mb
Running examples in ‘misc3d-Ex.R’ failed
The error most likely occurred in:

> ### Name: slices3d
> ### Title: Interactive Image Slices of 3D or 4D Volume Data
> ### Aliases: slices3d
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   #Example 1: View of a mixture of three tri-variate normal densities
>   nmix3 <- function(x, y, z, m, s) {
+       0.4 * dnorm(x, m, s) * dnorm(y, m, s) * dnorm(z, m, s) +
+       0.3 * dnorm(x, -m, s) * dnorm(y, -m, s) * dnorm(z, -m, s) +
+       0.3 * dnorm(x, m, s) * dnorm(y, -1.5 * m, s) * dnorm(z, m, s)
+   }
>   x<-seq(-2, 2, len=40)
>   g<-expand.grid(x = x, y = x, z = x)
>   v<-array(nmix3(g$x,g$y,g$z, .5,.5), c(40,40,40))
>   slices3d(vol1=v, main="View of a mixture of three tri-variate normals", col1=heat.colors(256))
Loading required package: tkrplot
Loading required package: tcltk
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Invalid MIT-MAGIC-COOKIE-1 keyWarning: loading Rplot failed
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: slices3d ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  13.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlbgameday.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlDNA.Rcheck/00install.out’ for details.
installed size is 41.9Mb
  sub-directories of 1Mb or more:
    chunks   3.4Mb
    libs    38.4Mb
Running examples in ‘mlmm-Ex.R’ failed
The error most likely occurred in:

> ### Name: mlmc
> ### Title: mlmc for missing and censored response in multilevel model.
> ### Aliases: mlmc
> 
> ### ** Examples
> 
> ## Don't show: 
> testfun=function()
+ {set.seed(100)
+  var2=abs(rnorm(50,0,1))
+  var1=(1/0.85)*var2;
+  geneid=rep(c(1:10),5);sid=c(rep(c(1:25),2),rep(c(26:50),2));
+  censor=rep(0,50)
+  pidname="geneid";sidname="sid";
+  miss_logit=var2*(-0.9);
+  miss=rbinom(50,1,exp(miss_logit)/(exp(miss_logit)+1));
+  censor=rep(0,50)
+  for (i in 1:50) {if (var1[i]<0.05) censor[i]=1}
+  for ( i in 1:50) {if ((miss[i]==1) & (censor[i]==1)) miss[i]=0};
+  for ( i in 1:50) {if (miss[i]==1) var1[i]=NA;
+  if (censor[i]==1) var1[i]=0.05}
+  pdata=data.frame(var1,var2,miss,censor,geneid,sid)
+  pathdir=getwd()
+  if (R.Version()$arch=="i386") fp=system.file("chunks","mlmc_i32.rds",package="mlmm")
+  if (R.Version()$arch=="x86_64") fp=system.file("chunks","mlmc_i64.rds",package="mlmm")
+  mcfit=readRDS(fp)
+  model1=mlmc(formula_completed=var1~var2,formula_missing=miss~var2,
+              formula_censor=censor~1,formula_subject=~var2,pdata=pdata,response_censorlim=0.05,
+              respond_dep_missing=TRUE,pidname="geneid",sidname="sid",pathname=pathdir,
+              iterno=10,chains=2,savefile=FALSE,usefit=TRUE,stanfit=mcfit)
+  }
> system.time(testfun())
Error in prep_call_sampler(object) : 
  the compiled object from C++ code for this model is invalid, possible reasons:
  - compiled with save_dso=FALSE;
  - compiled on a different platform;
  - does not exist (created from reading csv files).
Calls: system.time ... sampling -> .local -> <Anonymous> -> prep_call_sampler
Timing stopped at: 0.08 0.003 0.083 
Execution halted
Package required and available but unsuitable version: ‘mlr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘mlrMBO’
Found the following significant warnings:
  Warning: replacing previous import ‘BBmisc::isFALSE’ by ‘backports::isFALSE’ when loading ‘mlr’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mlr.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘mlrMBO’
Running the tests in ‘tests/run-base.R’ failed.
Last 13 lines of output:
  10: isTRUE(e$handled)
  11: e$handled
  12: `$.Throwable`(e, handled)
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2463 SKIPPED: 7 FAILED: 2
  1. Error: (unknown) (@test_base_clustering.R#14) 
  2. Error: (unknown) (@test_base_measures.R#112) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'mlt.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cf>
          O^^[<d7>^^V>^^]?DF"^^^<df>M<e5>и<b8>W/r<a4>X0<c8>R<a4><a2>"<b2>@<8a><ba><a1><ab><ae><da>u<fa>o<f4>/<e8><a2>j7<ac><bb><a8><84><94><85>wQ<bc><b0><85>J...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a4><a2>"<b2>@<8a><ba><a1><ab><ae><da>u<fa>o<f4>/<e8><a2>j7<ac><bb><a8><84><94><85>wQ<bc><b0><85>J<af>#<8d>-<82><a2>\<d9>
                                                  <9e>"^^W+p<99>	M<dd>T<d8>o<f1>=^^_MM<c0>^^FL...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...MM<c0>^^FL^^R<f3>|^^V<d6>x|<ef><99>{<e6>|<f7><dc><f3><de>k<b7><db>tu<c9>x<db><b8>\^^Z
                                                  <89>7<cc>4^^Ro<98>i$<de>0<d3>H<bc>a<a6><91>x<c3>L#<f1><88><88>...
The control sequen
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/modcmfitr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/modifiedmk.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 341 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 342 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 350 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'modTempEff.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...2^^F<e2><f5>2^^F<e2><f5>2<9e>m񤔏<bd>TJ<f1><cd>t:<dd>V<ad><c3><e3><96>eI)q<ff><e0>S<b9>\<ce>
                                                  ^^?<93><ab>^^U<8b>E^^?5<a5>^^T^^Z<f1>w<e3><b1>x...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<a5>¯l^^S<d2><ff><e0><c1>^^V<b8>p<f0><92><db><d9><da>ڪxxR<b3><a8>ӹ<e7><dd><c9>	~^^RQ<b9>\<fe>
                                                  <ec><b3><cf><c0>7"<92>R~<f7><dd>w<df>|<f3><cd>G^^_}t<fd><fa>u<d3>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.18 <84>L<a7>Ӧi<82><a5>^^_~<f8><e1><b5>k<d7>r<b9><9c>a^^XB^^H"<ca>f<b3>^^W.\^^X
                                             ^^Y^^Y<d1>4
The control sequence at the end of the top line
of your error message w
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MOEADr.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    1.6Mb
    libs   3.1Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    libs  13.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monogeneaGM.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/monoreg.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mopa.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.6Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 872 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'moult.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          o<db>F^^V^^?<96>[<cb>,^^RSD<82><ae><e2>]F^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 ...<cd><cd>o<be><f9><a6><c7><d4><fd>s<a6><d5><d5><d5>Z<ad>vD<83>^^G^^O^^^<9c><df><e8>c<fe>(<de>^^[\^^Z
                                                  r<f1><c6><ef>ܹs<ac>^^N<b7>o߾|<f9>r.<97>^^[^^_...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ..._<8f>F<a3><cb><cb>ˏ^^^=<92>eY^^P<84><c3><da>3Ʈ_<bf><9e><cd>f<af>_<bf><8e>[۶u]WUu}
                                                  }<bd>\.<a7>R)4VUUQ<94>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Errors in running code in vignettes:
when running code in ‘move.Rnw’
  ...

> load("a.Rdata")

> ggmap(m) + geom_path(data = leroy_df, aes(x = location.long, 
+     y = location.lat))

  When sourcing ‘move.R’:
Error: GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Error in re-building vignettes:
  ...
Loading required package: geosphere
Loading required package: sp
Loading required package: raster
Loading required package: rgdal
rgdal: version: 1.2-16, (SVN revision 701)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.2, released 2016/10/24
 Path to GDAL shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.1, 04 March 2015, [PJ_VERSION: 491]
 Path to PROJ.4 shared files: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/Rlib/3.3/rgdal/proj
 Linking to sp version: 1.2-5 
Warning in .local(x, y, time, data, proj, ...) :
  There were NA locations detected and omitted. Currently they are not stored in unusedrecords
Loading required package: ggmap
Loading required package: ggplot2
Loading required package: mapproj
Loading required package: maps

Error: processing vignette 'move.Rnw' failed with diagnostics:
 chunk 15 (label = googleplot) 
Error : GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msir.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/MSQC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/msu.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mtk.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘MASS’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyDesigner.sobol: no visible global function definition for ‘runif’
basicMonteCarlo: no visible global function definition for ‘runif’
lhs003: no visible global function definition for ‘runif’
plmm.mtk : GenereXplmm: no visible binding for global variable ‘poly’
plmm.mtk : calc.plm: no visible global function definition for ‘lm.fit’
plmm.mtk: no visible global function definition for ‘var’
plmm.mtk: no visible global function definition for ‘lm’
plmm.mtk: no visible global function definition for ‘formula’
plmm.mtk: no visible global function definition for ‘update’
plmm.mtk: no visible global function definition for ‘stepAIC’
plot.plmm: no visible global function definition for ‘par’
plot.plmm: no visible global function definition for ‘barplot’
plot.plmm: no visible global function definition for ‘segments’
plot.plmm: no visible global function definition for ‘abline’
plot.plmm: no visible global function definition for ‘title’
plot.plmm: no visible global function definition for ‘legend’
plot.regressionSI: no visible global function definition for ‘par’
plot.regressionSI: no visible global function definition for ‘title’
plot.regressionSI: no visible global function definition for ‘abline’
plot,mtkProcess: no visible global function definition for ‘dev.new’
Undefined global functions or variables:
  abline barplot dev.new formula legend lm lm.fit par poly runif
  segments stepAIC title update var
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "barplot", "legend", "par",
             "segments", "title")
  importFrom("stats", "formula", "lm", "lm.fit", "poly", "runif",
             "update", "var")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyNote: found 2 marked UTF-8 strings
Invalid MIT-MAGIC-COOKIE-1 keyNamespace in Imports field not imported from: ‘grDevices’
  All declared Imports should be used.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/mudfold.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'multgee.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<9a>J<a5>t]O<a5>R<e9>t<9a><88>8<e7>D<94>J<a5><88>(<93>ɤR)<b0><87>_WVV&&&^^XcW<ae>\<b9>
                                                  u<eb><d6>͛7^^Yc<9c>s<c6>^^X^^Q<c9>U<ee>ܹ<f3><f1>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...^XcW<ae>\<b9>u<eb><d6>͛7^^Yc<9c>s<c6>^^X^^Q<c9>U<ee>ܹ<f3><f1><c7>^^_sί\<b9>
                                                  <92><c9>d<ee>ܹs<ed>ڵt:<fd><cd>7<df>`<e4>n<d4><dc>7<cd><ce><ce>V...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<c3>@<9a><ae><eb><b8>Q^^@3 ^^G<f0>s<ce>u]<9f><9e><9e><ce>d2<f2><d6>^^A<a8><9d><ec><d9>^^G{ \?
                                                  <ec><e3>퐮뚦<ed><ed>Y<df><ec>u^^W<f5><f4>^7<93>^^O<bd>...
The control sequence a
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 70.9Mb
  sub-directories of 1Mb or more:
    libs  70.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/multinets.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 305 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 306 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 307 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Ch-Errata.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.34 ...<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}
                                                  Z<fa><b4><f4>i<e9><d3>ҧ<a5>OK<9f><96>>-}Z<fa><b4><f4>i<e9><d3>ҧ...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyconceptIndicesSkm: no visible global function definition for
  ‘txtProgressBar’
conceptIndicesSkm: no visible global function definition for
  ‘setTxtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘txtProgressBar’
conceptVectorsSkm: no visible global function definition for
  ‘setTxtProgressBar’
mvcmb: no visible global function definition for ‘runif’
mvcmb: no visible global function definition for ‘str’
mvcsph: no visible global function definition for ‘pdf’
mvcsph: no visible global function definition for ‘heatmap’
mvcsph: no visible global function definition for ‘dev.off’
mvcsph: no visible global function definition for ‘hclust’
mvcsph: no visible global function definition for ‘dist’
mvcsph: no visible global function definition for ‘str’
Undefined global functions or variables:
  dev.off dist hclust heatmap pdf runif setTxtProgressBar str
  txtProgressBar
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("stats", "dist", "hclust", "heatmap", "runif")
  importFrom("utils", "setTxtProgressBar", "str", "txtProgressBar")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
                    
! Illegal unit of measure (pt inserted).
<to be read again> 
                   \let 
l.979 \end{tabularx}
                    
! Missing number, treated as zero.
<to be read again> 
                   \let 
l.979 \end{tabularx}
                    
! Illegal unit of measure (pt inserted).
<to be read again> 
                   \let 
l.979 \end{tabularx}
                    
! Missing number, treated as zero.
<to be read again> 
                   \let 
l.979 \end{tabularx}
                    
! Illegal unit of measure (pt inserted).
<to be read 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyplot.matchedwake: no visible global function definition for
  ‘filled.contour’
plot.matchedwake: no visible binding for global variable ‘gray.colors’
plot.matchedwake: no visible global function definition for ‘axis’
plot.matchedwake: no visible global function definition for ‘rect’
slideWakeMatch: no visible binding for global variable ‘lm’
slideWakeMatch: no visible global function definition for ‘as.formula’
slideWakeMatch: no visible global function definition for ‘summary.glm’
Undefined global functions or variables:
  as.formula axis filled.contour gray.colors lm rect summary.glm
Consider adding
  importFrom("grDevices", "gray.colors")
  importFrom("graphics", "axis", "filled.contour", "rect")
  importFrom("stats", "as.formula", "lm", "summary.glm")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/My.stepwise.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nat.nblast.Rcheck/00install.out’ for details.
Running examples in ‘nat.nblast-Ex.R’ failed
The error most likely occurred in:

> ### Name: nblast
> ### Title: Calculate similarity score for neuron morphologies
> ### Aliases: nblast
> 
> ### ** Examples
> 
> # load sample Kenyon cell data from nat package
> data(kcs20, package='nat')
> # search one neuron against all neurons
> scores=nblast(kcs20[['GadMARCM-F000142_seg002']], kcs20)
> # scores from best to worst, top hit is of course same neuron
> sort(scores, decreasing = TRUE)
GadMARCM-F000142_seg002 ChaMARCM-F000586_seg002 GadMARCM-F000423_seg001 
              4043.1766               1914.8224               1772.8506 
GadMARCM-F000442_seg002 FruMARCM-M000115_seg001 FruMARCM-F000085_seg001 
              1007.4565                853.8108                713.2106 
FruMARCM-F001929_seg001 FruMARCM-F001494_seg002 GadMARCM-F000050_seg001 
               604.4071                481.4737                480.4146 
GadMARCM-F000071_seg001 FruMARCM-M001339_seg001 FruMARCM-F000188_seg001 
               448.1516                433.9340                404.0470 
GadMARCM-F000476_seg001 FruMARCM-F000270_seg001 FruMARCM-F000706_seg001 
               313.2021                254.7516                204.2116 
FruMARCM-M000842_seg002 FruMARCM-M001051_seg002 FruMARCM-M001205_seg002 
               196.4543                140.8164               -251.4999 
GadMARCM-F000122_seg001 FruMARCM-F001115_seg002 
              -262.2352               -520.2581 
> hist(scores, breaks=25, col='grey')
> abline(v=1500, col='red')
> 
> # plot query neuron
> open3d()
null 
   1 
> # plot top 3 hits (including self match with thicker lines)
> plot3d(kcs20[which(sort(scores, decreasing = TRUE)>1500)], lwd=c(3,1,1))
Error in xyz.coords(x, y, z, xlab = xlabel, ylab = ylabel, zlab = zlabel,  : 
  'x' is a list, but does not have components 'x', 'y'  and 'z'
Calls: plot3d -> plot3d.default -> xyz.coords
Execution halted
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because NBLAST-Clustering.Rmd appears to be an R Markdown v2 document.
Invalid MIT-MAGIC-COOKIE-1 keyQuitting from lines 56-59 (NBLAST-Clustering.Rmd) 
Error: processing vignette 'NBLAST-Clustering.Rmd' failed with diagnostics:
'x' is a list, but does not have components 'x', 'y'  and 'z'
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NB.MClust.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NeatMap.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keydata.reduction: no visible global function definition for ‘prcomp’
data.reduction: no visible global function definition for ‘hclust’
data.reduction: no visible global function definition for ‘as.dist’
data.reduction: no visible global function definition for ‘cor’
data.reduction: no visible global function definition for ‘dist’
heatmap1: no visible global function definition for ‘sd’
lineplot: no visible global function definition for ‘sd’
normalize: no visible global function definition for ‘sd’
profileplot3d : ColorFunction: no visible global function definition
  for ‘rgb’
profileplot3d : ColorFunction: no visible global function definition
  for ‘colorRamp’
profileplot3d: no visible global function definition for ‘sd’
profileplot3d: no visible global function definition for ‘gray’
Undefined global functions or variables:
  as.dist colorRamp cor dist gray hclust prcomp rgb sd
Consider adding
  importFrom("grDevices", "colorRamp", "gray", "rgb")
  importFrom("stats", "as.dist", "cor", "dist", "hclust", "prcomp", "sd")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neatmaps.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nesRdata.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.4Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   5.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Running examples in ‘network-Ex.R’ failed
The error most likely occurred in:

> ### Name: read.paj
> ### Title: Read a Pajek Project or Network File and Convert to an R
> ###   'Network' Object
> ### Aliases: read.paj read.paj.simplify switchArcDirection
> ###   readAndVectorizeLine
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> require(network)
> 
> par(mfrow=c(2,2))
> 
> test.net.1 <- read.paj("http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net")
Warning in file(file, "rt") :
  cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/GD/gd98/A98.net': HTTP status was '0 (null)'
Error in file(file, "rt") : cannot open the connection
Calls: read.paj -> file
Execution halted
Running the tests in ‘tests/read.paj_tests.R’ failed.
Last 13 lines of output:
  > 
  > 
  > 
  > # this file has character encoding issues
  > scotland<-tempfile('scotland',fileext='.zip')
  > download.file('http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip',scotland)
  trying URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  Error in download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  : 
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip'
  In addition: Warning message:
  In download.file("http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip",  :
    cannot open URL 'http://vlado.fmf.uni-lj.si/pub/networks/data/esna/scotland.zip': HTTP status was '0 (null)'
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/neuroim.Rcheck/00install.out’ for details.
installed size is 31.9Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              3.2Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nipals.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-68 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because trees_with_root_edge.Rmd appears to be an R Markdown v2 document.
Error: processing vignette 'vignette_get_nltt_values.Rmd' failed with diagnostics:
(converted from warning) It seems you should call rmarkdown::render() instead of knitr::knit2html() because vignette_get_nltt_values.Rmd appears to be an R Markdown v2 document.
Execution halted
Packages suggested but not available for checking: ‘RcppOctave’ ‘doMPI’
Package unavailable to check Rd xrefs: ‘RcppOctave’
Running examples in ‘NoiseFiltersR-Ex.R’ failed
The error most likely occurred in:

> ### Name: EF
> ### Title: Ensemble Filter
> ### Aliases: EF EF.default EF.formula
> 
> ### ** Examples
> 
> data(iris)
> # We fix a seed since there exists a random partition for the ensemble
> set.seed(1)
> out <- EF(Species~., data = iris, consensus = FALSE)
Error in .jnew("weka/core/Attribute", attname[i], .jcast(levels, "java/util/List")) : 
  java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Calls: EF ... read_model_frame_into_Weka -> read_data_into_Weka -> .jnew -> .External
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 190-198 (NoiseFiltersR.Rnw) 
Error: processing vignette 'NoiseFiltersR.Rnw' failed with diagnostics:
java.lang.UnsupportedClassVersionError: weka/core/Attribute : Unsupported major.minor version 51.0
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/nonlinearTseries.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/norm2.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NormalizeMets.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/NPCirc.Rcheck/00install.out’ for details.
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  11.6Mb
Error in re-building vignettes:
  ...
     
     taxi <- etl("nyctaxi", dir = "~/Desktop/nyctaxi/")
     taxi %>% 
        etl_extract(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_transform(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_load(years = 2016, months = 1:2, types = c("yellow","green")) 
     ## End(Not run)
     


Attaching package: 'lubridate'

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

    date

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotec1567ce40ba.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotec1567ce40ba.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/oaqc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OasisR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OceanView.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   2.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/odk.Rcheck/00install.out’ for details.
installed size is 85.7Mb
  sub-directories of 1Mb or more:
    libs  85.3Mb
Packages required and available but unsuitable versions:
  ‘stats’ ‘graphics’ ‘methods’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/onemap.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 359 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OneTwoSamples.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...^^G0X<b9>To<98><e5>R<bd>a<96>K<f5><86>Y.<d5>^^[f<b9>To<98><e5>o<af><9e>^^PB^^H<d1><fd>^
                                                  J)<84><98><9b><9b><8b>~<ed>.|૪<db>]<a5><bb><97>R<a9>$:^^R...
! Undefined control sequence.
l.16 ...A<a0><9e><89>h@^^Z<9e>^^]s<c2>J^^C<b5>U<b7>\:<86>a<96>><cc>Y*<95><ce>f^^\/"<b9>\<ee>
                                                  y<80><bf><e0><e0>^^\<b8><df>SR*<95><a4><94>o<be><f9><e6><f8><f8>x<b3><d9>L...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 ...a<9a><e6><d6>֖<aa><8e>q^^_Ѝs<ce>^^XS<9b><84> ^^H0^^W<f8><9a><c9>d<80>|h"<a5>\YY
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because ontologySimilarity-GO-example.Rmd appears to be an R Markdown v2 document.
Quitting from lines 46-49 (ontologySimilarity-GO-example.Rmd) 
Error: processing vignette 'ontologySimilarity-GO-example.Rmd' failed with diagnostics:
could not find function "intersection_with_descendants"
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenCL.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘mlr’

Package suggested but not available for checking: ‘farff’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OpenMPController.Rcheck/00install.out’ for details.
installed size is 149.0Mb
  sub-directories of 1Mb or more:
    R         1.8Mb
    libs    139.7Mb
    models    4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot527afa3951b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot527afa3951b.png': No such file or directory
Quitting from lines 22-24 (openwindfarm-vignette.Rmd) 
Error: processing vignette 'openwindfarm-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/optBiomarker.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyavg2Lower: no visible global function definition for ‘optimize’
classificationError.data.frame: no visible binding for global variable
  ‘na.omit’
classificationError.data.frame: no visible global function definition
  for ‘terms’
classificationError.data.frame: no visible binding for global variable
  ‘predict’
classpredict.lda: no visible global function definition for ‘predict’
simData: no visible global function definition for ‘rnorm’
simData: no visible global function definition for ‘runif’
simData: no visible global function definition for ‘var’
tnormAvg: no visible global function definition for ‘dnorm’
tnormAvg: no visible global function definition for ‘pnorm’
yapprox: no visible global function definition for ‘approx’
Undefined global functions or variables:
  approx dnorm na.omit optimize pnorm predict rnorm runif terms var
Consider adding
  importFrom("stats", "approx", "dnorm", "na.omit", "optimize", "pnorm",
             "predict", "rnorm", "runif", "terms", "var")
to your NAMESPACE file.
Package suggested but not available for checking: ‘org.At.tair.db’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      4.0Mb
Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, xtabs

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

    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘IsoGene’
Invalid MIT-MAGIC-COOKIE-1 keygenRidge: no visible global function definition for ‘plogis’
ordGene: no visible global function definition for ‘anova’
ordGene: no visible global function definition for ‘lm’
ordSelect: no visible binding for global variable ‘sd’
ordSmooth: no visible binding for global variable ‘sd’
plot.ordPen: no visible global function definition for ‘grey’
plot.ordPen: no visible global function definition for ‘devAskNewPage’
plot.ordPen: no visible global function definition for ‘plot’
plot.ordPen: no visible global function definition for ‘lines’
predict.ordPen: no visible global function definition for ‘plogis’
Undefined global functions or variables:
  anova devAskNewPage grey lines lm plogis plot sd
Consider adding
  importFrom("grDevices", "devAskNewPage", "grey")
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "anova", "lm", "plogis", "sd")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
  input string 411 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 412 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 420 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'dicom.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Al
           ^^SG^^W~<b1><89><cc>V<c2><de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9r<ab>P%<84>^^O<95>"...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<de>^^Q^^T<b6><a1>&<d6>J^^P<a4>D!<c2>B*H<91>s<f0>9<b7><dc>z<e6>^^D<87><f6>^^BG<ae>\9
                                                  r<ab>P%<84>^^O<95>".(>`YTj<a4>^^U<b6><eb>?-<b4>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 ...<83>/<be><f8>b^^O<8b>^^\<f0><d8><eb>61l^^W@y.<97>K<a5>R<d9>l<f6>ȑ#sss<b9>\nzz
                                                  :^^H<d9>B<88>d2^^Y<bc>Q<e5>+<df><f7><a3>Ѩi<9a>B^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running examples in ‘osi-Ex.R’ failed
The error most likely occurred in:

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  SSL certificate problem: Invalid certificate chain
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   3.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.4Mb
Error in re-building vignettes:
  ...
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in .local(x, ...) :
  The following sequence IDs are not in the dataset: 311, 222
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  replaced special characters in figure filename "figs/OutbreakTools-out.width==".8\\textwidth"" -> "figs/OutbreakTools-out.width___.8\\textwidth_"
Warning in (if (out_format(c("latex", "sweave", "listings"))) sanitize_fn else paste0)(path,  :
  dots in figure paths replaced with _ ("figs/OutbreakTools-out_width____8//textwidth_")
Warning: The shape palette can deal with a maximum of 6 discrete values because
more than 6 becomes difficult to discriminate; you have 11. Consider
specifying shapes manually if you must have them.
Warning: Removed 58 rows containing missing values (geom_point).
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Warning: `show_guide` has been deprecated. Please use `show.legend` instead.
Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=51.516439,-0.171146&zoom=14&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 1022-1023 (OutbreakTools.Rnw) 
Error: processing vignette 'OutbreakTools.Rnw' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/OutliersO3.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pafdR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PanJen.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/parlitools.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions: ‘libcoin’ ‘inum’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 419 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'party.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.18 !8<e7>hV*<95>p]<ad>V?<ff><fc><f3><f9><f9><f9>R<a9><84>^^A<a5>^^X<ed>v<fb><f2><e5><cb>B^^H!D<b9>\<fe>
                                                <f2><cb>/?<f9><e4><93>J<a5>r<e3><c6>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.19 ...^Uc,^^H^^B<c3>0<a0><<e7><e6><e6>*<95><ca><f8><f8><f8>G^^_}<d4>^^Oϧ|<ef><8d>}<f6><d9>g}
                                                  6<c5><fb>^^SB<f8><be><df>n<b7><a1>֛<cd>f*<95><8a><e3>xcc<a3><db>...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rootSolve’ which was already attached by Depends.
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘kinship2’ ‘tcltk’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘rootSolve’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyCall with DUP:
   .C("powerR", as.integer(numOffspring), as.integer(numParents), 
       as.integer(numFamilies), as.integer(additionalOffspringPhenos), 
       as.integer(ascertainment), as.integer(modelGen), as.integer(modelTest), 
       as.double(afreqMarker), as.double(penAA), as.double(penAB), 
       as.double(penBB), as.double(heritability), as.double(contsAscertainmentLower), 
       as.double(contsAscertainmentUpper), as.double(pDiseaseAlleleGivenMarkerAllele), 
       as.double(afreqDSL), as.double(qnorm(1 - alpha/2)), as.double(offset), 
       as.integer(numSim), as.integer(ITERATION_KILLER), result, 
       DUP = FALSE)
DUP is no longer supported and will be ignored.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pbdPROF.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 key.win.appendLog: no visible binding for global variable ‘lines’
plotMC : panel: no visible global function definition for ‘points’
plotMC: no visible global function definition for ‘pairs’
plotMC: no visible global function definition for ‘mtext’
plotMC: no visible global function definition for ‘axis’
plotMC: no visible global function definition for ‘par’
readADpaths: no visible global function definition for ‘read.table’
readRep: no visible global function definition for ‘read.table’
saveADpaths: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  axis lines mtext pairs par points read.table write.table
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "pairs", "par",
             "points")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   6.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcensmix.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PCRedux.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pcr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 399 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 400 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 408 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'pcse.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<cb>^^RB^^X<86><c1>^^X#<a2><a5><a5><a5><8f>^^_?r<ce>s<b9>^^\<e7>|ee<e5><fa><f5><eb><8c>1\<cd>
                                                  f<b3><85>BA<8e><8a>1v<ef>޽^^NC?<e8>E<96><97><97><8f>o0?...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...<ba><ae>^^GA^^@<ad><a8><e5>gu<af>^^^O<e0><d4>4<ad>M7EQ<a4>n^^X^^AΣ<a5>\ZXW
                                                  <9a><a6><95><cb>eιi<9a><ae><eb>b<b8><8e><e3>^^DA<c0>9<c7>^^B^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...b<b8><8e><e3>^^DA<c0>9<c7>^^B^^VB^^@<ae><ae><eb>B7<c3>0<e2><f1>8<b6>^^G<d7>uGFF\<d7>
                                                  E?݌<f9><ac><c0><f9><8d>0j^^O<e0>^^D~<a8>5u<98>^^\...
The control sequence at the end of
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs    5.3Mb
    share  11.9Mb
Running examples in ‘pedometrics-Ex.R’ failed
The error most likely occurred in:

> ### Name: vgmICP
> ### Title: Initial covariance parameters (ICP)
> ### Aliases: vgmICP
> 
> ### ** Examples
> 
> data(meuse, package = "sp")
> icp <- vgmICP(z = log(meuse$copper), coords = meuse[, 1:2])
Invalid MIT-MAGIC-COOKIE-1 keyWarning in fun(libname, pkgname) : couldn't connect to display ":0"
Error: Package(s) needed for this function to work but notinstalled: georob
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/perccalc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permGPU.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/permPATH.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/phenomap.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/photobiologyLEDs.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot76f569d6a006.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot76f569d6a006.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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pifpaf.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]="./webshot8bbb5488991b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot8bbb5488991b.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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pkggraph.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.9Mb
Package required and available but unsuitable version: ‘SummarizedExperiment’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/playwith.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plink.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plot3Drgl.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/plsRcox.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   2.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pointblank.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/polypoly.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/portes.Rcheck/00install.out’ for details.
File ‘PottsUtils/libs/PottsUtils.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘sw.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.
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 ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/powell.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'd_jss_paper.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...R,<89><ad>qI^J<a6>^^NT^^B<81>^^U6^^P<ac><f8><a5>^^O<c5>}n!<d4>^^O}
                                                  (<ec>e~h<fb>TJMa/3dx<b0>U^^O<83>b<b5>H^^Q...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<ec><e8>ڎ<e4>V<8a>~^^Xsu<ee>9<e7><9e><ef>~<df><f9><fe><9d><ef>v^^Y<86>^^A<ed><cb><f7><bd><80><e6><a2>C^
                                                  +<a3>C^+<a3>C^+<a3><cd>ɳ5d^^VJ)<e7><bc>!S^^...
! Extra }, or forgotten $.
l.15 ...<93>MXp<c3>`B<9e>^^?[<eb>1v<ff><f8><e7><a5>^^?W6^^?q<f9>'<d7>T<d7>i<d8><d4>7<bf>]<88><ad>}
                  
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyfnfam: no visible global function definition for ‘qnorm’
fx: no visible global function definition for ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘qnorm’
normplot : <local> : replot: no visible global function definition for
  ‘pnorm’
normplot : <local> : replot: no visible global function definition for
  ‘plot’
normplot : <local> : replot: no visible global function definition for
  ‘dnorm’
normplot : <local> : replot: no visible global function definition for
  ‘points’
normplot : <local> : replot: no visible global function definition for
  ‘lines’
normplot : <local> : regen: no visible global function definition for
  ‘rnorm’
normplot : <local> : regen: no visible global function definition for
  ‘rexp’
nsibs: no visible global function definition for ‘qnorm’
ntdt: no visible global function definition for ‘uniroot’
plotDom: no visible global function definition for ‘plot’
plotNsibs: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘plot’
plotNtdt: no visible global function definition for ‘lines’
plotNtdt: no visible global function definition for ‘legend’
ptdt: no visible global function definition for ‘optimize’
ptdt: no visible global function definition for ‘uniroot’
ptdt: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  dnorm legend lines optimize plot pnorm points qnorm rexp rnorm
  uniroot
Consider adding
  importFrom("graphics", "legend", "lines", "plot", "points")
  importFrom("stats", "dnorm", "optimize", "pnorm", "qnorm", "rexp",
             "rnorm", "uniroot")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  ‘KEGG.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’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PReMiuM.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/prim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘gurobi’ ‘Rsymphony’
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because PRISMA.Rmd appears to be an R Markdown v2 document.
Quitting from lines 31-43 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.3Mb
Found the following significant warnings:
  Warning: replacing previous import ‘bupaR::filter_attributes’ by ‘edeaR::filter_attributes’ when loading ‘processmapR’
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/processmapR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ProFit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PropClust.Rcheck/00install.out’ for details.
LastFirstDiscreteSparse: Error while checking: evaluation nested too
  deeply: infinite recursion / options(expressions=)?
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/proxy.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'countreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 <c4><eb>g^^Z<88><d7><cf>4^^P<af><9f>i <de>^^Q^^RB^^H!<8e>ޗR<aa><eb>B<a1><80>1RJ\<e0>
                                                o<b5>Z
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Undefined control sequence.
l.18 \K
       ?<d3><f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^<ad>V766^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Missing $ inserted.
<inserted text> 
                $
l.18 ...<f0><e7><9f>^^?~<fa><d1><d8><e5>R<ca>J<a5><b2><b3><b3><b3><b8><b8><b8><b8><b8><c8>9^^?<f8><f0><a1>m۷n<dd>::<9e>s^
         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/pseudo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/psychmeta.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 401 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 409 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 410 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 418 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'raschmix.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 <82>`ss3<97>˹<ae><9b>L&^^Q<85>^^PQ<b9>\<9e>
                            <99><99><b1>,+<9d>N<c3><ee><a3>?^^H<82><bd><bd>=vhRJ<c4>.<9e><e7><e5>r<b9>C<93><f3><f8>X,<86><c9>^^]ǉ^^N;rN...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...<b3><a8>nC!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6>
                                                  <d4>\<9e><9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>///<c7><e3>qM<d3>\...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 ...C!_<d7><ed><e8><be>͹<89><f7>V<e8><8c>`<ee>l<f5><b0><9b><c3>^^Z<a5><94><c2>"<a0>͡&<f6><ab>8g<e5>\<e6><d4>\<9e>
                                                  <9a><ae><fa>ꝑ<ae>y<9d><b3><8d>߃<a2>//
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/PsyControl.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  Memory [MB] prior|after|max(diff) : 62.4 | 62.1 | 64.1 (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 25.5Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Package suggested but not available for checking: ‘rCBA’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qle.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qpcR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtbase.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qtlc.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/qualpalr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/quanteda.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/QuantifQuantile.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 430 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'quantspec.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.21 ...[L=^^X^^L^^F<83>A<8e>Pض],^^V5M<b3>,<8b>]X0#<a5><c4>Z^^PQ<b9>\<b6>
                                                  ,+^^R<89>X<96><c5>^^A<8e>6<e9>E?{^^\e<e9>N^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...A<8e>6<e9>E?{^^\e<e9>N^^Nu^^V<8c><b0>,<8b><88>fff<d2><e9><b4>^^[c<a8>`<db>v<b9>\<8e>
                                                  D"<8c>Ir!VUU<80>
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 <a7>ޭ^^@<89>^^H<be>ҹ<b0>^^G<ca><e5>rSSS<b9>\<8e>
                               <88><e0>^^VY<96>utt4<<^^\^^L^^F<a5><94>^<af>^^W^^F4/^^G<e4>!<f7><80>r0<ef>>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.25 ...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/quickPlot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/quickregression.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2GUESS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2OpenBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\AL
           ^^[W^^S^^^^^L^^FL<8c><97><a7>^^R0N^^V̪nCq<8d><cb>V<88> ^^Q~UT<ad><9a>*<f4><92>S<a2><f6>ƥ<97><f6><94>^^^<a3>ޫ^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Extra }, or forgotten \endgroup.
l.18 ...Tf<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}
                                                  }<bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^...
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.18 ...f<92><95><d4>/<aa>^^@e<e1>p^^X9<ee><ec><ec><8c>D"<99>L<a6><b1><b1><f1><e5><97>_<ce>f<b3>O<9e><<d1>u}}}
                                                  <bd><b9><b9><b9><bf><bf>?<9f><cf>744,,,tww<af><ad><ad>577^^...
I've deleted a 
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R2STATS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 231 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 232 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 240 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'R2WinBUGS.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.17 ...^L^^L<e8><ba>N^^Hq8^^\8<ad><c7><e3>Y\\,^^V<8b><9d><9d><9d>o<bf><fd><b6>In^^O\<cb>
                                                  <b3>^^H<e3>o<^^^<a7><ba>gf^^H<f6>G,f<fe>]^^S...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<da>ڪiZOO<8f><a6>i<cb><cb><cb>^^V<8b>^^E^^@*<95>Jgg<a7><a2>(<8f>^^^=r:<9d><b9>\<ae>
                                                  V<ab><f5><f5><f5><cd><ce><ce><f6><f7><f7><ff><f6><db>o<ad><ad><ad>^^W/^^^D...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 <9d>?^^?^^^<eb>\N
                <a7>szz^^Z7^^A<ed>jqq<91><e7>yUU<91><b3>|><8f>\<86><c3>a<97>˅@^^\[^^X<86>!<84><9c>9s&<95>J<c5>b1Q^^T^^A<e0>...
The control sequence at the end of the top line
of your error message was neve
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/R330.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘rgl’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘lattice’ ‘leaps’ ‘rgl’ ‘s20x’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/railtrails.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rainbow.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rakeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/randomForestExplainer.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  OK: 0 SKIPPED: 0 FAILED: 9
  1. Error: rapidrake works for non-atomic, non-empty char vectors (@test-rapidrake.R#4) 
  2. Error: rapidrake returns a score when there is only one word in txt (@test-rapidrake.R#9) 
  3. Error: rapidrake works for txt without alpha chars (@test-rapidrake.R#14) 
  4. Error: rapidrake works when all txt is removed based on POS tags (@test-rapidrake.R#19) 
  5. Error: rapidrake can hanlde non-array params (@test-rapidrake.R#24) 
  6. Error: rapidrake removes stop words (@test-rapidrake.R#29) 
  7. Error: pos stopping works as expected (@test-rapidrake.R#34) 
  8. Error: word_min_char filtering works as expected (@test-rapidrake.R#41) 
  9. Error: phrase_delims works as expected (@test-rapidrake.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAppArmor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RAPTOR.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.7Mb
Packages suggested but not available for checking: ‘rggobi’ ‘RODBC’
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.5Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RBMRB.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcartocolor.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rCBA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcdk.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    libs  10.6Mb
Error in re-building vignettes:
  ...
Warning in (if (grepl("\\.[Rr]md$", file)) knit2html else if (grepl("\\.[Rr]rst$",  :
  It seems you should call rmarkdown::render() instead of knitr::knit2html() because RClone_qmsevpops.Rmd appears to be an R Markdown v2 document.
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
Invalid MIT-MAGIC-COOKIE-1 key.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyenterTableMHTest : onOK: no visible global function definition for
  ‘na.omit’
startStop: no visible global function definition for ‘na.omit’
Undefined global functions or variables:
  na.omit
Consider adding
  importFrom("stats", "na.omit")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘depthTools’ ‘tcltk’
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keycomputeMBD : OnOutput: no visible global function definition for
  ‘tkbutton’
computeMBD: no visible global function definition for ‘tkbutton’
computeMBD : OnPlot: no visible global function definition for
  ‘tkcanvas’
computeMBD : OnPlot: no visible global function definition for
  ‘tkbutton’
computeTmean: no visible global function definition for ‘tkcanvas’
computeTmean: no visible global function definition for ‘tkbutton’
computeTmean : onOK: no visible global function definition for ‘par’
plotCentralCurves: no visible global function definition for ‘tkcanvas’
plotCentralCurves: no visible global function definition for ‘tkbutton’
plotCentralCurves : onOK: no visible global function definition for
  ‘par’
Undefined global functions or variables:
  par tkbutton tkcanvas
Consider adding
  importFrom("graphics", "par")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘FrF2.catlg128’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘Rcmdr’ ‘multcomp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘tseries’
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘MASS’ ‘Rcmdr’ ‘TeachingDemos’ ‘abind’ ‘forecast’ ‘tseries’ ‘xts’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘abind’ ‘e1071’ ‘qcc’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Invalid MIT-MAGIC-COOKIE-1 keyPackages in Depends field not imported from:
  ‘ENmisc’ ‘Hmisc’ ‘Rcmdr’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyPackages 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.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.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
Invalid MIT-MAGIC-COOKIE-1 keyBOXWP: no visible binding for global variable ‘top’
BOXWP: no visible binding for global variable ‘buttonsFrame’
HIST: no visible binding for global variable ‘top’
HIST: no visible binding for global variable ‘buttonsFrame’
QQN: no visible binding for global variable ‘top’
QQN: no visible binding for global variable ‘buttonsFrame’
Undefined global functions or variables:
  buttonsFrame top
Invalid MIT-MAGIC-COOKIE-1 keyfncLRpROC: no visible global function definition for ‘palette’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncLRpROC : onOK : convert: no visible global function definition for
  ‘rgb’
fncPairedpROC: no visible global function definition for ‘palette’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncPairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncUnpairedpROC: no visible global function definition for ‘palette’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘col2rgb’
fncUnpairedpROC : onOK : convert: no visible global function definition
  for ‘rgb’
fncvpROC: no visible global function definition for ‘palette’
fncvpROC : onOK : convert: no visible global function definition for
  ‘col2rgb’
fncvpROC : onOK : convert: no visible global function definition for
  ‘rgb’
Undefined global functions or variables:
  col2rgb palette rgb
Consider adding
  importFrom("grDevices", "col2rgb", "palette", "rgb")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keySampleSizes: no visible global function definition for ‘xtabs’
SampleSizes: no visible global function definition for ‘weighted.mean’
SampleSizes: no visible global function definition for ‘reshape’
stage1Sample.fn: no visible global function definition for ‘runif’
stage2Sample.fn: no visible global function definition for ‘runif’
strata.options : onOK: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription reshape runif weighted.mean xtabs
Consider adding
  importFrom("stats", "reshape", "runif", "weighted.mean", "xtabs")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘SLC’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘SLC’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘car’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘RColorBrewer’ ‘Rcmdr’ ‘car’ ‘colorspace’ ‘vcd’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Invalid MIT-MAGIC-COOKIE-1 keyRcmdr.steeptestDij : onOK: no visible binding for global variable
  ‘replications’
Rcmdr.steeptestPij : onOK: no visible binding for global variable
  ‘replications’
Undefined global functions or variables:
  replications
Consider adding
  importFrom("stats", "replications")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘ROpenOffice’ ‘RODBC’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
    po    2.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rcplex.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppAPT.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    include   5.1Mb
    libs      1.7Mb
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.2Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.1Mb
Error in re-building vignettes:
  ...
  input string 420 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RcppEigen-Introduction.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...\(^^T<c2><e1>0<cf><f3>^^@@^^H<91>e<b9>Z<ad>F"<91><b3>j׻ջ<9c><f4><f7>v-^^Ly\f
                                                  <92>$<e9>$<b3><bf>6<ce>~<a6><f3>ƽ<ce>	<a1><f3><f8><f8><b8><db><ed>Fw<fa>^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.22 ...<ab>U^^@<e8>0^^[`t]k<b9><a2>t<ad>^?S^^W<a0><ec><db>o<bf><bd>u<eb><96> ^^H<b9>\^^N
                                                  <db>^^@<ad><d7>H<82> <e8><ba>^<af><d7>%Q<d4>^^?<fc>Q<98><9d>5t...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.26 <c3>H<a7>ӣ<a3><a3>XYs:<9d>SSSX<a1><e8><bd>zG<e8><fc><d5>!^^G<96>"^l<c6><c0>\<8b>
                                          <ae><eb><c5>b<f1><9d>w<de><c1>2D<eb>^^X\[Ji<a1>P^^@<80><fd><fd>}|^^E^^...
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 34.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      21.4Mb
    libs     11.0Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      7.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      5.2Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.2Mb
    libs      3.3Mb
Missing or unexported object: ‘tools::package_native_routine_registration_skeleton’
Error in re-building vignettes:
  ...
  input string 356 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 364 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 365 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 373 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Rcpp-jss-2011.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.20 ^^D^^B<f5>z^^]<dd><c0>j<88>C<^^^<cf>f<b3><fb>T*@^^O¹<ba><ba><ea><fd><f7>ڵk<b9>\<8e>
                                                <88>j<b5>Z<b1>X<84><b3><9f>J<a5><ea><f5><ba><97><<dc>3<c6>D4^^@<a0><9b><ae><eb>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.30 <c3> "x<8c><de>c^^]o<ad><84><cf><e7>^^S<89>Pj9<f2><9f><eb><eb><eb>^^W.\<c0>
                                       <b0><8e><e3>`X^^\<c7>{<8f>k0<88><f8>^^UƘa^^X8v<a3>FO|<eb><83><c9><dd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.30 ...<d1>."<86><a1><a1>!UU<e7><e7><e7><ab>ժ<b0><c2><e9>tztt<b4>T*<89><e8>[D^^^<b0><f8><86>a<f8><fd>~8\<8e>
                                                  <e3>^^H<bb><8f><c3><fa>j<b5><8a><88>N<84>^^Q<88><cd>m
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 88.1Mb
  sub-directories of 1Mb or more:
    include   4.4Mb
    lib      52.2Mb
    libs     31.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RcppTOML.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcrypt.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rcv.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RDieHarder.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rdoxygen.Rcheck/00install.out’ for details.
Running examples in ‘Rdrools-Ex.R’ failed
The error most likely occurred in:

> ### Name: Rdrools-package
> ### Title: A Rules Engine for R based on the popular Java based Drools
> ### Aliases: Rdrools-package Rdrools
> ### Keywords: rulesSession runRules Rdrools
> 
> ### ** Examples
> 
> library(Rdrools)
> data(class)
> data(rules)
> input.columns<-c('name', 'class', 'grade', 'email')
> output.columns<-c('address', 'subject', 'body')
> rules.session<-rulesSession(rules, input.columns, output.columns)
Error in .jnew("org/math/r/drools/DroolsService", rules, input.columns,  : 
  java.lang.UnsupportedClassVersionError: org/math/r/drools/DroolsService : Unsupported major.minor version 51.0
Calls: rulesSession -> .jnew -> .External
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]="./webshot10ed72e986034.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10ed72e986034.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 10.3Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.7Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("recurse")
  ── 1. Failure: move objects (@test_recurse.R#148)  ─────────────────────────────
  getRecursions(movePts, 1) not equal to getRecursions(simplePts, 1).
  Component "revisitStats": Component "id": Attributes: < Component "levels": 1 string mismatch >
  Component "revisitStats": Component "id": 5 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 143 SKIPPED: 1 FAILED: 1
  1. Failure: move objects (@test_recurse.R#148) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘RODBC’ ‘RODBCext’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/redlistr.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  14.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/redR.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycook.outliers: no visible global function definition for ‘lm’
cook.outliers: no visible global function definition for
  ‘cooks.distance’
nonparRI: no visible global function definition for ‘quantile’
plot.interval: no visible global function definition for ‘par’
plot.interval: no visible global function definition for ‘plot.new’
plot.interval: no visible global function definition for ‘plot.window’
plot.interval: no visible global function definition for ‘segments’
plot.interval: no visible global function definition for ‘axis’
plot.interval: no visible global function definition for ‘title’
plot.interval: no visible global function definition for ‘legend’
plot.interval: no visible global function definition for ‘box’
plot.interval: no visible global function definition for ‘text’
robust: no visible global function definition for ‘qt’
singleRefLimit: no visible global function definition for ‘qnorm’
singleRefLimit: no visible global function definition for
  ‘shapiro.test’
singleRefLimit: no visible global function definition for ‘ks.test’
Undefined global functions or variables:
  axis box cooks.distance ks.test legend lm par plot.new plot.window
  qnorm qt quantile segments shapiro.test text title
Consider adding
  importFrom("graphics", "axis", "box", "legend", "par", "plot.new",
             "plot.window", "segments", "text", "title")
  importFrom("stats", "cooks.distance", "ks.test", "lm", "qnorm", "qt",
             "quantile", "shapiro.test")
to your NAMESPACE file.
Running examples in ‘RefManageR-Ex.R’ failed
The error most likely occurred in:

> ### Name: WriteBib
> ### Title: Create a BibTeX File from a BibEntry Object e Creates a Bibtex
> ###   File from a BibEntry object for use with either BibTeX or BibLaTex.
> ### Aliases: WriteBib
> ### Keywords: IO
> 
> ### ** Examples
> 
> bib <- ReadCrossRef(query = '10.1080/01621459.2012.699793')
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 11000 milliseconds
Calls: ReadCrossRef ... request_fetch -> request_fetch.write_memory -> <Anonymous> -> .Call
Execution halted
Error in re-building vignettes:
  ...
  input string 84 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 85 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 93 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'registry.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>[Ok^^S<dd>^^W>o<fa><ab><b5>Pf<bc> <b1>(i<ea>l*^^H5<a5> <a5>P<c6>EvBw<ee>\<fb>
                                                 1<c4>m<bf><82>[wfe<b1><b8><b0><9b><f8>'Be ^^]<82>]^^H^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<a2>J<a5>2??<af><94><9a><9e><9e><f6>}?<97><cb><d5>j5۶]<d7><c5>x!^^D^^C^^X^^Qv<b9>\<ce>
                                                  <e5>r<f8>Y<ad>V-<cb><c2><e4><fc>^^W7<c3>0<b4>,<ab><95>+0^^@...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ...<c7>h<b1>2O<8c><ba>u<eb>X[)^^E<ac>Ǌ<b8>ID<bb><bb><bb><90>^^V<88>ª<b0><b1>@,<cb><d0>h4\<d7>
                                                  <85>E
The control sequence at the end of the top line
of your error message was
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reportROC.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  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: clipboard input works (@test-input.R#12) 
  5. Error: reprex: expression input works (@test-input.R#17) 
  6. Error: reprex: character input works (@test-input.R#23) 
  7. Error: reprex: file input works (@test-input.R#31) 
  8. Error: reprex: file input in a subdirectory works (@test-input.R#40) 
  9. Error: Circular use is detected before render (@test-input.R#47) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/reshapeGUI.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘S4Vectors’

Package suggested but not available for checking: ‘rsolr’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/restlos.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyGUI_template : onHelp: no visible global function definition for ‘help’
Undefined global functions or variables:
  help
Consider adding
  importFrom("utils", "help")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Error: processing vignette 'methodbehind_reverseengineeringcensus.ltx' failed with diagnostics:
Running 'texi2dvi' on 'methodbehind_reverseengineeringcensus.ltx' failed.
LaTeX errors:
! Undefined control sequence.
l.54 ...ted to approximate $\lambda$\textsubscript
                                                  {3}, which subsequently pr...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.54 ...ides the necessary $\lambda$\textsubscript
                                                  {1} and $\lambda$\textsubs...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.54 ...xtsubscript{1} and $\lambda$\textsubscript
                                                  {2} parameters. The estima...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
Execution halted
installed size is 36.6Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 102.7Mb
  sub-directories of 1Mb or more:
    libs      100.2Mb
    pictures    1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rgeopat2.Rcheck/00install.out’ for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rggobi.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc     3.1Mb
    fonts   1.5Mb
    libs    6.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rgnuplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key
(R:76308): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘gWidgetsRGtk2’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘RGtk2’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running examples in ‘RGtk2Extras-Ex.R’ failed
The error most likely occurred in:

> ### Name: gtkDfEdit
> ### Title: gtkDfEdit
> ### Aliases: gtkDfEdit [.gtkDfEdit [<-.gtkDfEdit RGtk2DfEdit
> 
> ### ** Examples
> 
>   win <- gtkWindowNew()

(R:2383): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:2383): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:2383): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:2383): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

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

Traceback:
 1: .Call(name, ..., PACKAGE = PACKAGE)
 2: .RGtkCall("S_gtk_widget_show_all", object, PACKAGE = "RGtk2")
 3: gtkWidgetShowAll(w)
 4: gtkWindowNew()
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning: It seems you should call rmarkdown::render() instead of knitr::knit2html() because intro_rhandsontable.Rmd appears to be an R Markdown v2 document.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rhmmer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rhpc.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls in package code:
  ‘doMC’ ‘doSNOW’ ‘e1071’ ‘fftw’ ‘foreach’ ‘jpeg’ ‘png’ ‘rggobi’
  ‘tkrplot’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘parallel’ ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Codoc mismatches from documentation object 'c,Medline-method':
\S4method{c}{Medline}
  Code: function(x, ..., recursive = FALSE)
  Docs: function(x, ...)
  Argument names in code not in docs:
    recursive
Invalid MIT-MAGIC-COOKIE-1 keyrite : loadHistory: no visible global function definition for
  ‘savehistory’
rite : saveGist: no visible global function definition for ‘browseURL’
rite : uploadToRPubs : processEntry: no visible global function
  definition for ‘browseURL’
rite : runCode: no visible global function definition for ‘savehistory’
rite : runCode: no visible global function definition for ‘loadhistory’
rite : knittxt: no visible global function definition for ‘Sweave’
rite : knittxt: no visible global function definition for ‘browseURL’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘packageDescription’
rite : addHighlighting : addHighlight: no visible global function
  definition for ‘na.omit’
rite : about : <anonymous>: no visible global function definition for
  ‘browseURL’
rite : <anonymous>: no visible global function definition for
  ‘capture.output’
rite : <anonymous>: no visible global function definition for
  ‘update.packages’
rite : <anonymous>: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help’
rite : f1: no visible global function definition for ‘help.search’
rite : commandCompletion: no visible global function definition for
  ‘apropos’
rite : findreplace : <anonymous>: no visible global function definition
  for ‘browseURL’
Undefined global functions or variables:
  Sweave apropos browseURL capture.output help help.search loadhistory
  na.omit packageDescription savehistory update.packages
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "Sweave", "apropos", "browseURL", "capture.output",
             "help", "help.search", "loadhistory", "packageDescription",
             "savehistory", "update.packages")
to your NAMESPACE file.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/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 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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RkMetrics.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘golubEsets’
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLakeAnalyzer.Rcheck/rLakeAnalyzer/doc/data.handling.R':
invalid multibyte character in parser at line 20
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rLindo.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RMark.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RmecabKo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmetasim.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rmgarch.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    libs  13.9Mb
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   
  +   # 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 ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rmpi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RnavGraph.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
Running examples in ‘RnavGraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: ng_get_color
> ### Title: Extract point coloring from an active navGraph session for a
> ###   particular data set.
> ### Aliases: ng_get_color
> 
> ### ** Examples
> 
> ## Define a NG_data object
> ng.iris <- ng_data(name = "IrisData", data = iris[,1:4])
> 
> ## start a navGraph session
> nav <- navGraph(ng.iris)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: navGraph ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Errors in running code in vignettes:
when running code in ‘RnavGraph.Rnw’
  ...
> sel <- sample(x = 1:11000, size = 600)

> p.digits <- digits[, sel]

> ng.i.digits <- ng_image_array_gray("USPS Handwritten Digits", 
+     p.digits, 16, 16, invert = TRUE, img_in_row = FALSE)

  When sourcing ‘RnavGraph.R’:
Error: [tcl] invalid command name "image".
Execution halted
Error in re-building vignettes:
  ...
    Filter, Find, Map, Position, Reduce, anyDuplicated, append,
    as.data.frame, cbind, 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, rownames, sapply, setdiff, sort, table, tapply, union,
    unique, unsplit

Invalid MIT-MAGIC-COOKIE-1 keyWarning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

RnavGraph Version 0.1.8
Please read the package vignette. Use vignette("RnavGraph").


Invalid MIT-MAGIC-COOKIE-1 keyWarning in tclRequire("Img") : Tcl package 'Img' not found
Can not load the tk Img extension. Hence you can not use the 'ng_image_files' R function. Read the package vignette on how to set up tcl/tk.
Loading required package: grid

Error: processing vignette 'RnavGraph.Rnw' failed with diagnostics:
 chunk 57 
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "image".

Execution halted
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
installed size is 95.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     93.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rNOMADS.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 547 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 548 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 556 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RobPer_vignette.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[G^^[^^?,<bf><ae><ba>`K^^Y^^B<89>P<ea>j<bb>PhIP<9d><ee>%<84>^^V<e5><a0>R<e8>!<b7><fc>^^C<a5><e4>_p<8f>9<94>B.=<b6>Đ<d2>^^F...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...^z^^ZrՒ^^@N8<c1><ff>r<b2>m{'<88><8e><c0>9Ȕ֥<de>?<c1><8d>~<f3><cd>7s<b9>\^^T
                                                  EP<98><87>=萃<b3><bf><dd>CD<83>B<ab>՚<9e><9e><c6>'^^QE...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.20 <e3><d6>n<b7><d1>^^E^^?<a5>-^^C^^U^^D<c1><cc>̌<ef><fb><b9>\^^N
                                      <f5><ad>V<cd>,˂<89>c<9e>(<97><cb>e!^^D<8f>hY<96>뺨L<9c>p^^_g<cf><f7>}^^...
The control sequence at the end of the top line
of your error message was never \def'ed. I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

> ### Name: rbwheel
> ### Title: Multivariate Barrow Wheel Distribution Random Vectors
> ### Aliases: rbwheel
> ### Keywords: distribution robust
> 
> ### ** Examples
> 
> set.seed(17)
> rX8 <- rbwheel(1000,8, fullResult = TRUE, scaleAfter=FALSE)
> with(rX8, stopifnot(all.equal(X, X0 %*% A,    tol = 1e-15),
+                     all.equal(X0, X %*% t(A), tol = 1e-15)))
> ##--> here, don't need to keep X0 (nor A, since that is Qrot(p))
> 
> ## for n = 100,  you  don't see "it", but may guess .. :
> n <- 100
> pairs(r <- rbwheel(n,6))
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## for n = 500, you *do* see it :
> n <- 500
> pairs(r <- rbwheel(n,6))
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> ## but increasing sig2 does help:
> pairs(r <- rbwheel(n,6, sig2 = .2))
> 
> ## show explicitly
> n1 <- attr(r,"n1") ; pairs(r, col=1+((1:n) > n1))
> 
> set.seed(12)
> pairs(X <- rbwheel(n, 7, spherize=TRUE))
> colSums(X) # already centered
[1] -3.129441e-15  6.151329e-15 -8.555656e-15  2.352285e-15  2.428613e-16
[6]  3.505876e-15 -3.537101e-15
> 
> if(require("ICS")) {
+   # ICS: Compare M-estimate [Max.Lik. of t_{df = 2}] with high-breakdown :
+   stopifnot(require("MASS"))
+   X.paM <- ics(X, S1 = cov, S2 = function(.) cov.trob(., nu=2)$cov, stdKurt = FALSE)
+   X.paM.<- ics(X, S1 = cov, S2 = function(.) tM(., df=2)$V, stdKurt = FALSE)
+   X.paR <- ics(X, S1 = cov, S2 = function(.) covMcd(.)$cov, stdKurt = FALSE)
+   plot(X.paM) # not at all clear
+   plot(X.paM.)# ditto
+   plot(X.paR)# very clear
+ }
Loading required package: ICS
Loading required package: mvtnorm
Loading required package: MASS
Error in S2(c(0.906882501852091, -2.27769597461744, -1.05320504986729,  : 
  could not find function "covMcd"
Calls: ics -> do.call -> S2
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RockFab.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RODBC.Rcheck/00install.out’ for details.
Package required but not available: ‘RODBC’

Package suggested but not available for checking: ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ROracle.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rotations.Rcheck/00install.out’ for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.7Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rothermel.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keybestFM: no visible global function definition for ‘data’
gaRoth: no visible global function definition for ‘data’
ros: no visible global function definition for ‘na.omit’
rosunc: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  data na.omit rnorm
Consider adding
  importFrom("stats", "na.omit", "rnorm")
  importFrom("utils", "data")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpanel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RPEnsemble.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so':
  dlopen(/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so, 6): Symbol not found: _GSS_C_NT_HOSTBASED_SERVICE
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so
  Expected in: flat namespace
 in /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so
Error: package or namespace load failed for ‘rpg’
Execution halted
Error in dyn.load(file, DLLpath = DLLpath, ...) : 
  unable to load shared object '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so':
  dlopen(/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so, 6): Symbol not found: _GSS_C_NT_HOSTBASED_SERVICE
  Referenced from: /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so
  Expected in: flat namespace
 in /Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpg.Rcheck/rpg/libs/rpg.so
Calls: <Anonymous> ... eval -> eval -> loadNamespace -> library.dynam -> dyn.load
Execution halted

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

Probably some imports need to be declared in the NAMESPACE file.
Error: package or namespace load failed for ‘rpg’
Call sequence:
2: stop(gettextf("package or namespace load failed for %s", sQuote(package)), 
       call. = FALSE, domain = NA)
1: library(package, lib.loc = lib.loc, character.only = TRUE, verbose = FALSE)
Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rpicosat.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rpoppler.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘graphics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  18.0Mb
Error in re-building vignettes:
  ...
  input string 348 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 354 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'RProtoBuf-paper.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.23 ...<a2>i^^ZVn3*<80><b0>^^X<89>^^H8<e5>ryqq<b1>^^W<d3><d2>_PV<af><d7>MӔۃ\<c9>
                                                  [<bd>^<cf>f<b3><9f>}<f6><99>i<9a><b0><ae><a0>,<93><c9>lmm<c9>w<a4>iZ...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.24 ...<af><d7>q^^T^^Yc<d3><d3><d3>D<e4><fb>>^^Q<c1>^^?<f4><de><e5>^^[<a4>r<b6><a9><d6>Q<9a><f6>"<8b>e}
                                                  X<ce>|><8f><bc><f8><d0>V^^Nc^^L6
I've deleted a group-closing symbol because it seems to be
spurious, as in `$x}$'. But perhaps the } is legitimate and
! Extra }, or forgotten \endgroup.
l.25 ^^AW&<93>	^^G<96>
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsample.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSAP.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/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.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsgcc.Rcheck/00install.out’ for details.
installed size is 27.4Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
Package required and available but unsuitable version: ‘S4Vectors’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  45.6Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rSQM.Rcheck/00install.out’ for details.
installed size is 123.6Mb
  sub-directories of 1Mb or more:
    doc     2.4Mb
    libs  119.7Mb
installed size is 282.5Mb
  sub-directories of 1Mb or more:
    libs  280.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsurface.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rsurfer.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RSwissMaps.Rcheck/RSwissMaps/doc/vignette.R':
invalid multibyte character in parser at line 20
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/Rsymphony.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Package required but not available: ‘keyholder’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RunuranGUI.Rcheck/00install.out’ for details.
installed size is 32.5Mb
  sub-directories of 1Mb or more:
    libs  31.9Mb
Missing or unexported object: ‘xml2::xml_find_first’
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘pixmap’ which was already attached by Depends.
  Please remove these calls from your code.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyrvideopoker: warning in rp.radiogroup(mypanel, var =
  state$penny.nickel.quarter.dollar, initval = 1, values = c(1, 5, 25,
  100), title = "Bet (in Cents)", action = setbet): partial argument
  match of 'var' to 'variable'
rvideopoker: warning in rp.slider(mypanel, var = state$no.of.credits,
  from = 1, to = 5, initval = 1, title = "How many Credits?",
  resolution = 1, action = creditset, showvalue = TRUE): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC1, action = card1check, title = "Keep Card 1?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC2, action = card2check, title = "Keep Card 2?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC3, action = card3check, title = "Keep Card 3?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC4, action = card4check, title = "Keep Card 4?"): partial
  argument match of 'var' to 'variable'
rvideopoker: warning in rp.checkbox(panel = mypanel, var =
  state$keepC5, action = card5check, title = "Keep Card 5?"): partial
  argument match of 'var' to 'variable'
rvideopoker : plotFrame: no visible global function definition for
  ‘par’
rvideopoker : showBack: no visible global function definition for
  ‘title’
rvideopoker : showCardsInitially: no visible global function definition
  for ‘title’
Undefined global functions or variables:
  par title
Consider adding
  importFrom("graphics", "par", "title")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rvinecopulib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RVPedigree.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/RWekajars.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘RWekajars’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/rWind.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' call to ‘vcd’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘foreign’ ‘ggplot2’ ‘grid’ ‘psych’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Unexported object imported by a ':::' call: ‘foreign:::adQuote’
  See the note in ?`:::` about the use of this operator.
Invalid MIT-MAGIC-COOKIE-1 keycalc.hist.breaks: no visible global function definition for
  ‘nclass.Sturges’
calc.hist.breaks: no visible global function definition for ‘nclass.FD’
calc.hist.breaks: no visible global function definition for
  ‘nclass.scott’
check.class: no visible global function definition for ‘as.formula’
gtkColorSelectionForPlotGetColor: no visible global function definition
  for ‘rgb’
gtkColorSelectionWidgetNew: no visible global function definition for
  ‘colors’
gtkFileChooserDialogFilteredActivate: no visible binding for global
  variable ‘theme_grey’
localize: no visible global function definition for ‘localeToCharset’
summary.CrossTable : twoDimTable: no visible global function definition
  for ‘addmargins’
summary.CrossTable: no visible global function definition for
  ‘assocstats’
write.spss: no visible global function definition for ‘write.table’
write.stata: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  addmargins as.formula assocstats colors localeToCharset nclass.FD
  nclass.Sturges nclass.scott rgb theme_grey write.table
Consider adding
  importFrom("grDevices", "colors", "nclass.FD", "nclass.Sturges",
             "nclass.scott", "rgb")
  importFrom("stats", "addmargins", "as.formula")
  importFrom("utils", "localeToCharset", "write.table")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/samplesizeCMH.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'sandwich-CL.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ml
           ^^S<c9>^^R.b o<a4>`<d3>^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 !^^D.>|<f8>p<e8><d0>!<d3>4<85>^^P<a6>i<b6><e9><f9><be>osAd<db>6<94><ff>B<e9><d6><f6>"(<fa>\^^E
                                                <80>S/<b7>m<9b>om}^^\3<b6><b5>A<a0>c<eb>[<b8><b0>T*uD&u...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.17 ...c<eb>[<b8><b0>T*uD&u	N<f4><a9>X,<e2>^^E<d3><d3>Ӹf^^A<e4><84>^^PJ)۶o߾}
                                                  <eb><d6>-^^T^^R^^QP<84>^^V>~<fc>x<ec><d8>1`^...
I
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/scanstatistics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 5):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following objects are masked from stature (pos = 6):

    election, opponent, opponent.height, opponent.party,
    opponent.vote, turnout, winner, winner.bmi, winner.height,
    winner.party, winner.vote

The following object is masked from package:SciencesPo:

    turnout

.data was converted to a dataframe
Warning: New theme missing the following elements: axis.line.x, axis.line.y, panel.grid.major, panel.grid.minor
Quitting from lines 1090-1091 (SciencesPo.Rmd) 
Error: processing vignette 'SciencesPo.Rmd' failed with diagnostics:
invalid 'times' argument
Execution halted
Error in re-building vignettes:
  ...
  input string 355 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 356 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 364 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 {[[[/_<be><9c><99><99><c9><e5>r<e9>tZ)<a5><94>z<fa><f4><e9><9d>;wr<b9>ܽ{<f7><d0>f||\^^H
                                             <81><e9><89><e8><ed>۷<c9>d<f2>ɓ'<c9>dR^^H<a1><94>ZYY<e1>u+<a5><84>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.19 ...\^^H<81><e9><89><e8><ed>۷<c9>d<f2>ɓ'<c9>dR^^H<a1><94>ZYY<e1>u+<a5><84>^^P+++<b9>\<8e>
                                                  <ff>J)
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.31 <f9>^^F"<c2>y^^T"<ac><d4>G!<c2>B\R
                        <ca>ǯ<94>꯿<e4>￧<89>><b2><dd>ǼKKK<d0>p<bc><93>^^L^^V#<cb>{<ea><bb>wn)<d8>)<e3><af>^<84>V<<ba><b3><b3>399...
The control sequence at the end of the top line
of your error message was never \def'ed. If you h
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 62 SKIPPED: 0 FAILED: 7
  1. Failure: examples: all examples (@test_api_stability.R#156) 
  2. Failure: examples: all examples (@test_api_stability.R#157) 
  3. Failure: examples: all examples (@test_api_stability.R#162) 
  4. Failure: execute: valid command (@test_execute.R#13) 
  5. Failure: execute: valid commands (@test_execute.R#18) 
  6. Failure: execute: runner provided (@test_execute.R#64) 
  7. Failure: execute: print_commands (@test_execute.R#69) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SDD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sdols.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/selectiveInference.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Error in re-building vignettes:
  ...
  input string 439 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 447 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 448 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 456 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'semPLS-intro.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ...<f4><af>i<9a>^^X<a2><94>m<db>['<8c>^^N<e9><85><de><eb><fd>ư<b0><b0><c0>^^X<b3>,<eb><e4>ɓW<ae>\1
                                                  M<f3><fe><fd><fb>W<af>^^^UB<98><a6><f9><f8><f1><e3><c9><c9>I<a5>T<bd>^<bf>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 ^^E^^\^^R<c2>^^[<fe>.,,<80>^^Y<a5><d4><e5>˗<a5><94>+++<b6>m^^S\<95>
                                           RB<88><f9><f9><f9>~<ad><a7><cf>ҋK<c4><d2>><cd><ff><8e><d9><db>o^^ZڽA<a6>=<a9>^^...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 <82>?s<b9><94>m<bb><8d><c6><fb><9c>^^_<e5><fc>^^?^^WS<c3>0<94>R<8e><e3><cc><ce>΢^^Ec<b1>\<f2>
                                             E<a4><94><89>Db}}}bb<a2><d9>l&^^R<89>f<b3>)<84><a8>T
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sentometrics.Rcheck/00install.out’ for details.
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    doc    6.0Mb
    libs  10.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sergeant.Rcheck/00install.out’ for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Package suggested but not available for checking: ‘lwgeom’
installed size is 137.6Mb
  sub-directories of 1Mb or more:
    doc      10.1Mb
    libs    123.7Mb
    sqlite    1.5Mb
Package unavailable to check Rd xrefs: ‘lwgeom’
Running examples in ‘sf-Ex.R’ failed
The error most likely occurred in:

> ### Name: geos_measures
> ### Title: Compute geometric measurements
> ### Aliases: geos_measures st_area geos_measures st_length geos_measures
> ###   st_distance
> 
> ### ** Examples
> 
> b0 = st_polygon(list(rbind(c(-1,-1), c(1,-1), c(1,1), c(-1,1), c(-1,-1))))
> b1 = b0 + 2
> b2 = b0 + c(-0.2, 2)
> x = st_sfc(b0, b1, b2)
> st_area(x)
[1] 4 4 4
> line = st_sfc(st_linestring(rbind(c(30,30), c(40,40))), crs = 4326)
> st_length(line)
Error in st_length(line) : 
  package lwgeom required, please install it first
Execution halted
Running the tests in ‘tests/dist.R’ failed.
Last 13 lines of output:
  > 
  > y = st_sfc(
  + st_point(c(0,10)),
  + st_point(c(1,0)),
  + st_point(c(2,0)),
  + st_point(c(3,0)),
  + st_point(c(4,0)),
  + crs = 4326
  + )
  > 
  > d.sf = st_distance(x, y)
  Error in st_distance(x, y) : lwgeom required: install first?
  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 795-797 (sf1.Rmd) 
Error: processing vignette 'sf1.Rmd' failed with diagnostics:
package lwgeom required, please install it first
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shadowtext.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/shinyRGL.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SIBER.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sidier.Rcheck/00install.out’ for details.
randomDAG: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  rbinom
Consider adding
  importFrom("stats", "rbinom")
to your NAMESPACE file.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SimCop.Rcheck/00install.out’ for details.
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  10.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   3.4Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/skeleSim.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/slam.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions: ‘stats’ ‘parallel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 438 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'smacof.tex' failed.
LaTeX errors:
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.15 ...<a5>^^_<a0><af><fd>^^D}+<81><d0>B<a1>)^^T^^D<85><fa><cd>T^^T^^Y<e3>Bڻ )F<89>^
                                                  <86>]-Eر3޵<e2><ec>ub<f9>><fc>аqbKJ<ac>$<d2><d5>...
! Undefined control sequence.
l.19 ^^Y{<fd>҈#g<f2><9b>o<be>^^Y<d0><d0>w<ee><dc>^^QB<ec><ee><ee><ea><ba><fe><e3><8f>?^<bf>~<bd>P(\<bb>
                                               vM<fd>>{<f6>lcc<e3><87>^^_~<f0><OJ<d9>;<cc><f6>N#<ae><9c>o<8a>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 ...<9a><a6>9<d0>8^^]4<96><de>K^^D{<e5><fb>~:<9d><a6>X<d6>^^H<b1>^^Y^^Q<f9><be>OD<b9>\NJ
                         
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smbinning.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   5.9Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/smoothtail.Rcheck/00install.out’ for details.
Warning: parse error in file '/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/snakecase.Rcheck/snakecase/doc/caseconverters.R':
invalid multibyte character in parser at line 18
contact_matrix: possible error in xtabs(data = contacts.sample, formula
  = weight ~ agegroup + cnt.agegroup, addNA = TRUE): unused argument
  (addNA = TRUE)
contact_matrix: possible error in xtabs(data = part.sample, formula =
  weight ~ agegroup, addNA = TRUE): unused argument (addNA = TRUE)
Running examples in ‘socialmixr-Ex.R’ failed
The error most likely occurred in:

> ### Name: contact_matrix
> ### Title: Generate a contact matrix from diary survey data
> ### Aliases: contact_matrix
> 
> ### ** Examples
> 
> data(polymod)
> contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 1, 5, 15))
Using Polymod Social Contact Data. To cite this in a publication, use the 'cite' function
Sampling the age of contacts with missing age from other participants of the same age group.
  To change this behaviour, set the 'missing.contact.age' option
Error in xtabs(data = contacts.sample, formula = weight ~ agegroup + cnt.agegroup,  : 
  unused argument (addNA = TRUE)
Calls: contact_matrix -> xtabs
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
      doi = {10.5281/zenodo.1059920},
      publisher = {Zenodo},
      note = {Version 1.1},
      year = {2017},
    }
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 7 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test-matrix.r#13) 
  2. Error: surveys can be downloaded (@test-surveys.r#10) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-58 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unused argument (addNA = TRUE)
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/soundgen.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sourceR.Rcheck/00install.out’ for details.
Running examples in ‘SPACECAP-Ex.R’ failed
The error most likely occurred in:

> ### Name: SPACECAP
> ### Title: Fits spatially-explicit capture recapture models
> ### Aliases: SPACECAP
> 
> ### ** Examples
> 
> SPACECAP()
Invalid MIT-MAGIC-COOKIE-1 keyError in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SPACECAP ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Package required but not available: ‘quickPlot’

Package suggested but not available for checking: ‘SpaDES.tools’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshotc2412bdcf402.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2412bdcf402.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
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparseEigen.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparseHessianFD.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sparseMVN.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SpatialAcc.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spatialEco.Rcheck/00install.out’ for details.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    4.7Mb
    help   5.0Mb
    libs   1.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  14.8Mb
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: 'lgamma' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SPECIES.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spectrolab.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Warning in grid.Call(L_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sphereplot.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyPackage in Depends field not imported from: ‘rgl’
  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:
  ...
  input string 415 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'UsingSpikeSlabGAM.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<c1>
          k^^[W^^S<9f>H5<89><88>><ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D<fd>z<ed><b5><87><9e>K}O...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.15 ...<ad>^^_	qm<b3><de><f5><83>^^^<fa><d5><c8>^^B^^]J^^N<a9>|0^^T<f7><90>[(<f4>\^^D
                                                  <fd>z<ed><b5><87><9e>K}O/<ba><f9><d0>@<bd>^^D;<82><86><84>,]<ab>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Extra }, or forgotten \endgroup.
l.15 ...^D^^V<ad>^^WU<95><a9><fd><bc>k<c5>]<b7>X<fa>^^N?4<ec><e7>ږ<94>ڎ<e5>j^^Nb<f5><f6
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spotifyr.Rcheck/00install.out’ for details.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sprint.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spTDyn.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  11.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spTimer.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/spup.Rcheck/00install.out’ for details.
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: SRRS ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/ss3sim.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SSN.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SSRMST.Rcheck/00install.out’ for details.
Packages required but not available: ‘stacomirtools’ ‘RODBC’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/standardize.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    include   8.7Mb
    lib       1.1Mb
Error in re-building vignettes:
  ...
  Running 'texi2dvi' on 'StatCharrms.tex' failed.
LaTeX errors:
! Too many }'s.
l.351 ...tion}{Other Endpoints Specification Tab}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! Too many }'s.
l.455 ...oc}{subsection}{Other Endpoints Results}}
                                                  
You've closed more groups than you opened.
Such booboos are generally harmless, so keep going.
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.##
                   ##..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character #' in horizontal mode.
<argument> Lower.####
                     ..CI
l.485 			\item \textbf{Lower.##..CI}
                                    : The lower 1-alpha percent (defaults to...
! You can't use `macro parameter character
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/StatDA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/stddiff.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

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
Quitting from lines 220-233 (Details.Rmd) 
Error: processing vignette 'Details.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyDetailOpLines: 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
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  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
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    libs  30.6Mb
Running examples in ‘subspaceMOA-Ex.R’ failed
The error most likely occurred in:

> ### Name: DSC_HDDStream
> ### Title: Density-based Projected Clustering over High-Dimensional Data
> ### Aliases: DSC_HDDStream
> 
> ### ** Examples
> 
> dsc <- DSC_HDDStream()
Error in rJava::.jcall("moa/r_interface/OneStageClusterer", returnSig = "Lmoa/r_interface/RCompatibleDataStreamClusterer;",  : 
  RcallMethod: cannot determine object class
Calls: DSC_HDDStream -> <Anonymous> -> .External
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SUMMER.Rcheck/00install.out’ for details.
Package required but not available: ‘d3r’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/support.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/surveydata.Rcheck/00install.out’ for details.
installed size is 64.7Mb
  sub-directories of 1Mb or more:
    libs  64.0Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/survivalMPL.Rcheck/00install.out’ for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Invalid MIT-MAGIC-COOKIE-1 keydlgMessage.tcltkGUI: no visible global function definition for ‘alarm’
Undefined global functions or variables:
  alarm
Consider adding
  importFrom("utils", "alarm")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 keyprocessSocket: no visible global function definition for ‘URLdecode’
Undefined global functions or variables:
  URLdecode
Consider adding
  importFrom("utils", "URLdecode")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
  Warning: 'erfc' declared at (1) is also the name of an intrinsic.  It can only be called via an explicit interface or if declared EXTERNAL.
  Warning: Possible change of value in conversion from REAL(8) to INTEGER(4) at (1)
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1)
  apply.f:86:0: warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  burnop.f:29:0: warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:166:0: warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  harvestop.f:195:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvgrainop.f:168:0: warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  harvkillop.f:175:0: warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  plantop.f:87:0: warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:171:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1)
  sweep.f:56:0: warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
  rewind_init.f:172:0: warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/SWATmodel.Rcheck/00install.out’ for details.
Package required but not available: ‘timetk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/sybilSBML.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 426 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'symmoments.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\Ol
           ^^S<cb>^^Y<ff>b;^^?^^\<c0><bb>+^^^<90><86>8<b1><b6><e5>E<b4><c1><a1><b2>z^^H^^R5<95>,UBꡕ,<bd>'<ae>O^^QG<de>^^A<e5>^^]...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.16 <e9>j^^Op<b9>\<82>
               <94><ac><aa><a2><de><d7>^^?<fc>à<89>f<b3><db><d0>y<88><eb><d2>-f=<99><d1>M]<dd>9<bd><b3><a7><fb><f0><f6><f7><f1>o<be><f2>5A<e0><86><a1><8a>zg<b7><95>.=<f7><e7><bf><fe><fb>?<e9><cd>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.16 ...<9e><be>x<f1><a2>,<cb>^^V<8b><85><e7><
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tactile.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘GISTools’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    3.9Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.1Mb
Invalid MIT-MAGIC-COOKIE-1 keyaniplotevents: no visible global function definition for ‘plot’
aniplotevents: no visible global function definition for ‘lines’
cbfs: no visible global function definition for ‘rnorm’
cbfs: no visible global function definition for ‘runif’
cbfs_red: no visible global function definition for ‘arima.sim’
cbfs_red: no visible global function definition for ‘runif’
eventCluster: no visible global function definition for ‘princomp’
eventCluster: no visible global function definition for ‘kmeans’
measures: no visible global function definition for ‘sd’
measures: no visible global function definition for ‘var’
measures: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘Box.test’
noiseTests: no visible global function definition for ‘PP.test’
noiseTests: no visible global function definition for ‘ar’
plotevents: no visible global function definition for ‘plot’
plotevents: no visible global function definition for ‘lines’
ur.za.fast : roll: no visible global function definition for ‘coef’
ur.za.fast : roll: no visible global function definition for ‘lm’
Undefined global functions or variables:
  Box.test PP.test ar arima.sim coef kmeans lines lm plot princomp
  rnorm runif sd var
Consider adding
  importFrom("graphics", "lines", "plot")
  importFrom("stats", "Box.test", "PP.test", "ar", "arima.sim", "coef",
             "kmeans", "lm", "princomp", "rnorm", "runif", "sd", "var")
to your NAMESPACE file.
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tensorr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/termstrc.Rcheck/00install.out’ for details.
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs       6.9Mb
    tessdata  31.0Mb
Found the following significant warnings:
  Warning: Installed Rcpp (0.12.12) different from Rcpp used to build dplyr (0.12.11).
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tetraclasse.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 398 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'texreg.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x<9c><ed>\<cd>
          k^^[<d7>^^V?<95><f2><d1>!A<d2>}-AQQ,.^^D<c3>Kp^^D^^C<85>^^Z<8a>C0Y4P^^J
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.18 RJ<a5><94>^^P^^BS<e7><f3>y)<a5><e3>8B^^H<c3>0<94>R/^
                                 <bc>8s<e6><cc>ݻw<85><82>^^P<c2>4M)<e5><ec>쬮<eb><85>B<81><88><a4><94>RJ<d3>4<85>^^PJ<a9><d5><d5><d5>...
! Please use \mathaccent for accents in math mode.
\add@accent ...@spacefactor \spacefactor }\accent 
                                                  #1 #2\egroup \spacefactor ...
l.21 ...<8b>MMM^^]dÃa<ce>a<db>VG<86><c3>1<a7><94>ҶmP	<e4><c2>/3-^^X<8c>y<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.5Mb
    libs   4.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/texteffect.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘quanteda’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/textTinyR.Rcheck/00install.out’ for details.
Packages required and available but unsuitable versions:
  ‘parallel’ ‘phyloseq’ ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  x[4]: "#   <chr>, b <lgl>"
  y[4]: "#   a <chr>, b <lgl>"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 442 SKIPPED: 0 FAILED: 5
  1. Failure: trunc_mat output matches known output (@test-trunc-mat.R#21) 
  2. Failure: trunc_mat output matches known output (@test-trunc-mat.R#26) 
  3. Failure: trunc_mat output matches known output (@test-trunc-mat.R#31) 
  4. Failure: trunc_mat output matches known output (@test-trunc-mat.R#46) 
  5. Failure: trunc_mat output matches known output (@test-trunc-mat.R#61) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tidyboot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tidyhydat.Rcheck/00install.out’ for details.
Package required but not available: ‘rsample’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tidystats.Rcheck/00install.out’ for details.
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: augment(stm_model, dat) at testthat/test-stm-tidiers.R:59
  2: augment.STM(stm_model, dat)
  3: cast_dfm(data, document, term, value)
  4: quanteda::as.dfm(m)
  5: stop("as.dfm only applicable to matrix(-like) objects.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 218 SKIPPED: 0 FAILED: 2
  1. Error: Can cast tables into a sparse dfm (@test-sparse-casters.R#73) 
  2. Error: can augment an stm output (@test-stm-tidiers.R#59) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
The following objects are masked from 'package:stats':

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "book"
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Warning: Removed 896 rows containing non-finite values (stat_bin).
Warning 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: NLP

Attaching package: 'NLP'

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

    annotate

Quitting from lines 95-115 (tidying_casting.Rmd) 
Error: processing vignette 'tidying_casting.Rmd' failed with diagnostics:
as.dfm only applicable to matrix(-like) objects.
Execution halted
Package suggested but not available for checking: ‘treeio’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tidytree.Rcheck/00install.out’ for details.
Package required but not available: ‘reprex’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Running examples in ‘timetk-Ex.R’ failed
The error most likely occurred in:

> ### Name: tk_augment_timeseries
> ### Title: Augment the time series signature to the data
> ### Aliases: tk_augment_timeseries tk_augment_timeseries_signature
> 
> ### ** Examples
> 
> library(tidyquant)
Loading required package: lubridate

Attaching package: ‘lubridate’

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

    date

Loading required package: quantmod
Loading required package: xts
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

Loading required package: TTR
Version 0.4-0 included new data defaults. See ?getSymbols.
Loading required package: tidyverse
Loading tidyverse: ggplot2
Loading tidyverse: tibble
Loading tidyverse: tidyr
Loading tidyverse: readr
Loading tidyverse: purrr
Loading tidyverse: dplyr
Conflicts with tidy packages ---------------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: ‘tidyquant’

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

    as_tibble

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

    as_tibble

> library(timetk)
> 
> FANG %>%
+     filter(symbol == "FB") %>%
+     tk_augment_timeseries_signature()
Error in eval(expr, envir, enclos) : object 'FANG' not found
Calls: %>% -> eval -> eval
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: (unknown) (@test_tk_make_future_timeseries.R#46)  ─────────────────
  object 'FANG' not found
  1: FANG %>% filter(symbol == "FB") %>% tk_index() at testthat/test_tk_make_future_timeseries.R:46
  2: eval(lhs, parent, parent)
  3: eval(expr, envir, enclos)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 219 SKIPPED: 0 FAILED: 2
  1. Error: (unknown) (@test_tk_augment_timeseries.R#5) 
  2. Error: (unknown) (@test_tk_make_future_timeseries.R#46) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Conflicts with tidy packages ----------------------------------------------
as.difftime(): lubridate, base
date():        lubridate, base
filter():      dplyr, stats
first():       dplyr, xts
intersect():   lubridate, base
lag():         dplyr, stats
last():        dplyr, xts
setdiff():     lubridate, base
union():       lubridate, base

Attaching package: 'tidyquant'

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

    as_tibble

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

    as_tibble

Quitting from lines 57-64 (TK00_Time_Series_Coercion.Rmd) 
Error: processing vignette 'TK00_Time_Series_Coercion.Rmd' failed with diagnostics:
no applicable method for 'rename_' applied to an object of class "logical"
Execution halted
drawGraph: no visible global function definition for ‘eqmcc’
drawGraph: no visible global function definition for ‘pdf’
drawGraph: no visible global function definition for ‘par’
drawGraph: no visible global function definition for ‘plot’
drawGraph: no visible global function definition for ‘segments’
drawGraph: no visible global function definition for ‘lines’
drawGraph: no visible global function definition for ‘text’
drawGraph: no visible global function definition for ‘dev.off’
drugRank: no visible global function definition for ‘aggregate’
floating2: no visible global function definition for ‘cor’
timma: no visible global function definition for ‘median’
timma: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  aggregate cor dev.off eqmcc lines median par pdf plot segments text
  write.table
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "lines", "par", "plot", "segments", "text")
  importFrom("stats", "aggregate", "cor", "median")
  importFrom("utils", "write.table")
to your NAMESPACE file.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘MASS’ ‘boot’ ‘lattice’ ‘splines’ ‘tcltk’
  Please remove these calls from your code.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tkrgl.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyPackages 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.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 key.my.tkdev: no visible global function definition for ‘X11’
tkpersp : draw: no visible global function definition for ‘par’
tkpersp : draw: no visible global function definition for ‘persp’
Undefined global functions or variables:
  X11 par persp
Consider adding
  importFrom("grDevices", "X11")
  importFrom("graphics", "par", "persp")
to your NAMESPACE file.
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Running examples in ‘tm.plugin.dc-Ex.R’ failed
The error most likely occurred in:

> ### Name: tm_map.DCorpus
> ### Title: Transformations on Distributed Corpora
> ### Aliases: tm_map.DCorpus
> 
> ### ** Examples
> 
> data("crude")
> tm_map(as.DCorpus(crude), content_transformer(tolower))
Warning in file(con, "w") :
  cannot open file '/var/folders/8q/c881c7rn7_x34vj58f4ywhvm0000h3/T//Rtmpb0djBE/DSL-20160505-034420-gjoxfxyrqb/chunk-15dc814df4a7b': No such file or directory
Error in file(con, "w") : cannot open the connection
Calls: tm_map ... DS_write_lines -> <Anonymous> -> <Anonymous> -> file
Execution halted
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  ── 3. Error: (unknown) (@test-session.R#3)  ────────────────────────────────────
  tmux not found
  1: stop("tmux not found") at testthat/test-session.R:3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-pipe.R#3) 
  2. Error: (unknown) (@test-server.R#3) 
  3. Error: (unknown) (@test-session.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TNC.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 key'library' or 'require' calls to packages already attached by Depends:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  Please remove these calls from your code.
'library' or 'require' calls in package code:
  ‘TeachingDemos’ ‘ash’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Packages in Depends field not imported from:
  ‘Cairo’ ‘RGtk2’ ‘colorspace’ ‘gWidgets’ ‘tourr’
  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:
  ...
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading toxplot
No methods found in "RSQLite" for requests: dbGetQuery
We recommend that you use the dev version of ggplot2 with `ggplotly()`
Install it with: `devtools::install_github('hadley/ggplot2')`
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot5dd26b9b4530.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot5dd26b9b4530.png': No such file or directory
Quitting from lines 134-136 (Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd) 
Error: processing vignette 'Using_ToxPlot_Package_to_Analyze_in_vitro_Screening_Data.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2

Attaching package: 'trackeR'

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

    append

Map from URL : http://maps.googleapis.com/maps/api/staticmap?center=57.157231,-2.104296&zoom=13&size=640x640&scale=2&maptype=terrain&language=en-EN&sensor=false
Quitting from lines 90-91 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
GeomRasterAnn was built with an incompatible version of ggproto.
Please reinstall the package that provides this extension.
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TrajDataMining.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 1 representative(s) selected, coverage=46% (threshold=35%)
 [>] 88 distinct sequence(s)
 [>] number of objects (sum of weights): 196.82
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 4 representative(s) selected, coverage=39% (threshold=35%)
 [>] 148 distinct sequence(s)
 [>] number of objects (sum of weights): 99.22
 [>] max. distance: 139.84
 [>] neighborhood radius: 13.98
 [>] 5 representative(s) selected, coverage=38% (threshold=35%)
 [>] 89 distinct sequence(s)
Warning in readLines(log, warn = FALSE) :
  invalid input found on input connection 'TraMineR-state-sequence.log'
Warning in readLines(con, warn = FALSE) :
  invalid input found on input connection 'TraMineR-state-sequence.log'
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'TraMineR-state-sequence.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.15 x
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Packages required and available but unsuitable versions:
  ‘grid’ ‘phyloseq’ ‘stats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TreeSearch.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/treethresh.Rcheck/00install.out’ for details.
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tRophicPosition.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/trustOptim.Rcheck/00install.out’ for details.
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 ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tsBSS.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSCS.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘TSodbc’ ‘RODBC’
Packages unavailable to check Rd xrefs: ‘TSodbc’, ‘RODBC’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
Jan 10, 2018 1:56:07 PM 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]]
Jan 10, 2018 1:56:07 PM 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
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: getTSE
> ### Title: Download Historical Dataset from Tehran Stock Exchange (TSE)
> ### Aliases: getTSE
> 
> ### ** Examples
> 
> 	fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> 	assets0<-getTSE(fpath)$assets
proceeding...
Warning in download.file(temp, file1, mode = "wb", quiet = TRUE) :
  unable to connect to 'www.tsetmc.com' on port 80.
Error in download.file(temp, file1, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://www.tsetmc.com/tsev2/data/Export-txt.aspx?t=i&a=1&b=0&i=39453972158399542'
Calls: getTSE -> download.file
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Downloading GitHub repo RamiKrispin/TSstudio@master
from URL https://api.github.com/repos/RamiKrispin/TSstudio/zipball/master
Installing TSstudio
'/Library/Frameworks/R.framework/Resources/bin/R' --no-site-file  \
  --no-environ --no-save --no-restore --quiet CMD INSTALL  \
  '/private/tmp/RtmpeXgjW4/devtools14c7852a0b98e/RamiKrispin-TSstudio-99c5fce'  \
  --library='/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/TSstudio.Rcheck'  \
  --install-tests 

* installing *source* package ‘TSstudio’ ...
** R
** preparing package for lazy loading
** help
*** installing help indices
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (TSstudio)
Quitting from lines 30-53 (TSstudio_Intro.Rmd) 
Error: processing vignette 'TSstudio_Intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/tuber.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    doc         2.2Mb
    dummydata   1.4Mb
    libs       20.7Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/unfoldr.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   2.4Mb
Running examples in ‘uplift-Ex.R’ failed
The error most likely occurred in:

> ### Name: checkBalance
> ### Title: Standardized Differences for Stratified Comparisons
> ### Aliases: checkBalance
> ### Keywords: uplift xBalance
> 
> ### ** Examples
> 
> library(uplift)
> 
> set.seed(12345)
> dd <- sim_pte(n = 1000, p = 20, rho = 0, sigma =  sqrt(2), beta.den = 4)
> dd$treat <- ifelse(dd$treat == 1, 1, 0) 
> 
> checkBalance(treat ~ X1 + X2 + X3 + X4 + X5 + X6 , data = dd)
     strata  unstrat                                                              
     stat    treat=0  treat=1 adj.diff adj.diff.null.sd std.diff     z            
vars                                                                              
X1          0.01152  -0.00596 -0.01748         0.06006  -0.01840 -0.29103         
X2          0.03160  -0.02812 -0.05972         0.06236  -0.06057 -0.95778         
X3          0.01145  -0.02242 -0.03387         0.06355  -0.03370 -0.53303         
X4          0.01533  -0.03551 -0.05083         0.06370  -0.05046 -0.79801         
X5          -0.06440 0.02370  0.08810          0.06153  0.09060  1.43175          
X6          0.02237  -0.02177 -0.04414         0.06308  -0.04425 -0.69980         
---Overall Test---
        chisquare df p.value
unstrat      4.54  6   0.604
---
Signif. codes:  0 ‘***’ 0.001 ‘** ’ 0.01 ‘*  ’ 0.05 ‘.  ’ 0.1 ‘   ’ 1 
Error in ncol(DT) : object 'DT' not found
Calls: <Anonymous> ... withOptions -> tryCatch -> do.call -> <Anonymous> -> ncol
Execution halted
installed size is 68.8Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Package which this enhances but not available for checking: ‘lumberjack’
Unknown package ‘lumberjack’ in Rd xrefs
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vanddraabe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VarfromPDB.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error in re-building vignettes:
  ...
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 428 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 429 is invalid in this locale
Warning in grepl("(Rerun to get|biblatex.*\\(re\\)run)", readLines(log,  :
  input string 437 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'vars.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.16 ?<f1><8b><96><eb><96>;<d9>l6^^V<8b>uM<<c3>0n޼<99>N<a7>1\Y
                                 <96><f1><a6><96><fb><9a><a6><a5>R)<88>^^Z<8f><c7><f9>D^^D<83><c1>D"<a1><eb><ba>,˲,뺎6<f8><9a>J<a5>^^N...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.17 <bd>MMM<e1><9a>c^^?^^?<ff><ee>ݻ^^O^^_><9c><9b><9b><8b><c7>㌱<d9><d9>Y<bc><e8>$^^L\<cc>
                                                <84>H<d7><f5><d3><c7><dd>!<ba>,<9e><ae><eb>D<f4><e1><87>^^_z<9e>G<c7><fa><a1>cB...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.21 0<c6>X<b5>ZE\<e6>
             <a7>.<98>L<c7>[H~n<c7><e3>q<90><b6><a5>^^_<f4><cf>?<fd>!<de>)<8c><b8><88><a6><a5><8b>^^\n<e3>^^X^^Xc<b0>^^G|<c7>^^X^^[<94><f3><f3><f3>t<ec>	^...
The control sequence at the end o
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   2.9Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vcov.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VDA.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keycv.vda.le.default: no visible global function definition for ‘predict’
cv.vda.r.default: no visible global function definition for ‘predict’
Undefined global functions or variables:
  predict
Consider adding
  importFrom("stats", "predict")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VecStatGraphs3D.Rcheck/00install.out’ for details.
Invalid MIT-MAGIC-COOKIE-1 keyInvalid MIT-MAGIC-COOKIE-1 keyDrawDensity3D: no visible global function definition for ‘colorRamp’
DrawDensity3D: no visible global function definition for ‘rgb’
ReadFromFile3D: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  colorRamp read.table rgb
Consider adding
  importFrom("grDevices", "colorRamp", "rgb")
  importFrom("utils", "read.table")
to your NAMESPACE file.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/vegclust.Rcheck/00install.out’ for details.
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
installed size is 26.5Mb
  sub-directories of 1Mb or more:
    libs  26.1Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/VGAM.Rcheck/00install.out’ for details.
Running examples in ‘VisuClust-Ex.R’ failed
The error most likely occurred in:

> ### Name: FuzzyPlot
> ### Title: Displays a Fuzzy Plot
> ### Aliases: FuzzyPlot
> 
> ### ** Examples
> 
> 
> library(cluster)
> library(MASS)
> 
> # The example data
> data("MilchSmall")
> 
> M <- scale(MilchSmall[3:6])
> D <- dist(M)
> S <- sammon(D)
Initial stress        : 0.00738
stress after  10 iters: 0.00227, magic = 0.500
stress after  20 iters: 0.00204, magic = 0.500
stress after  30 iters: 0.00203, magic = 0.500
> F <- fanny(D, 6)
> 
> FuzzyPlot(S$points, F$membership, labels=MilchSmall[,2], 
+ 	clusterColors=c("red", "green", "magenta", "yellow", "blue", "black"))
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: FuzzyPlot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/visvow.Rcheck/00install.out’ for details.
installed size is 51.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs  48.8Mb
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wand.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/water.Rcheck/00install.out’ for details.
Running examples in ‘wbsts-Ex.R’ failed
The error most likely occurred in:

> ### Name: tau.fun
> ### Title: Universal thresholds
> ### Aliases: tau.fun
> ### Keywords: threshold
> 
> ### ** Examples
>  
> 
> cps=c(400,470)
> set.seed(101)
> y=sim.pw.ar(N =2000,sd_u = 1,b.slope=c(0.4,-0.6,0.5),br.loc=cps)[[2]]
> #tau.fun(y) is the default value for C_i
> #Binary segmentation
> wbs.lsw(y,M=1)$cp.aft
NULL
> #Wild binary segmentation
> wbs.lsw(y,M=3500)$cp.aft
Error in while (ind.max < 0 | ind.max > e) { : 
  missing value where TRUE/FALSE needed
Calls: wbs.lsw -> uh.wbs
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/webglobe.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/websearchr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WeightIt.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/weightr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/whereport.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wktmo.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WMCapacity.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(4) to INTEGER(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wnominate.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/woeR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/wooldridge.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
  input string 432 is invalid in this locale
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WRS2.tex' failed.
LaTeX errors:
! Undefined control sequence.
l.19 ...VB<e0>+W^^L<ce>O?<fd>^^T^^X[^^&"<ec>^^G"<82>p<e5>rYJ	<81><98>x&<b9>\<ce>
                                                  <f3><bc>d2	A<85>^^PA^^P<94>J%<f4><80>^^[<ef>g<a5>T...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! Undefined control sequence.
l.23 <95>l<f1><81><93>T*<85>ꥮ<eb>^^T<b9>^^]<88>sv<df><f7><85>^^P<cb><cb>˨^^Qan<9c><d7>an\2
                                                <8b><a6>s<b6>m+<a5><82>  "]<d7><f9><e4><bd><d1>h^^Pѩ<ca><ea>)<fa><b0>...
The control sequence at the end of the top line
of your error message was never \def'ed. If you have
! LaTeX Error: Missing \begin{document}.

See the LaTeX manual or LaTeX Companion for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Missing $ inserted.
<inserted text> 
                $
l.29 èV<ab><8b><8b><8b>tb<
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/WufooR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/x12GUI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: Possible change of value in conversion from REAL(8) to REAL(4) at (1)
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xbreed.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: get_comic(comic = 614) at testthat/test-tibble_creation.R:4
  2: httr::GET(url)
  3: request_perform(req, hu$handle$handle)
  4: request_fetch(req$output, req$url, handle)
  5: request_fetch.write_memory(req$output, req$url, handle)
  6: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: getcomics  (@test-tibble_creation.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    java   9.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
newXMLDoc: no visible binding for global variable ‘doc’
xmlFlatListTree : f: no visible binding for global variable ‘nodeNames’
xmlFlatListTree : f: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeSet’
xmlFlatListTree : addNode: no visible binding for global variable ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘nodeNames’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘idx’
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  ‘parentCount’
xmlFlatListTree : addNode: no visible binding for global variable
  ‘parentCount’
xmlFlatListTree : <anonymous>: no visible binding for global variable
  ‘e’
xmlFlatTree : <anonymous>: no visible binding for global variable ‘e’
[[,XMLCodeFile: possible error in updateIds(doc, save = x): unused
  argument (save = x)
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xptr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xray.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/xtensor.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YplantQMC.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/YuGene.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Builds/CRAN-QA-Simon/packages/mavericks-x86_64/results/3.3/zstdr.Rcheck/00install.out’ for details.