File ‘svmpath/libs/svmpath.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_eifr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi30spec.o’, ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi10unix.o’, ‘mi35mps.o’, ‘mi40bfil.o’

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

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

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

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

Traceback:
 1: .Primitive(".C")(<pointer: fd8105f0>, mat0 = as.double(mat0),     mat = as.double(mat), nsim = as.integer(nsim), recursive = as.integer(recursive),     nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(Kb),     Kt = as.integer(Kt), strata = as.integer(strata), perms = as.double(perms))
 2: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 3: swapClass_swapC(mat0 = as.double(mat0), mat = as.double(mat),     nsim = as.integer(nsim), recursive = as.integer(recursive *         1), nr = as.integer(nr), nc = as.integer(nc), Kb = as.integer(burnin),     Kt = as.integer(thin), strata = as.integer(strata), perms = as.double(perms))
 4: nullModel(MAT)
An irrecoverable exception occurred. R is aborting now ...
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2

Attaching package: 'Hmisc'

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

    format.pval, units

Quitting from lines 44-45 (HTML.Rmd) 
Error: processing vignette 'HTML.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Running examples in ‘tabplot-Ex.R’ failed
The error most likely occurred in:

> ### Name: -.tabplot
> ### Title: Compare two tableplots (experimental)
> ### Aliases: -.tabplot
> 
> ### ** Examples
> 
> # load diamonds dataset from ggplot2
> require(ggplot2)
Loading required package: ggplot2
> data(diamonds)
> 
> # calculate normalized prices to be used as sample probabilities
> price.norm <- with(diamonds, price / max(diamonds$price))
> 
> # draw samples
> exp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=price.norm, replace=TRUE),]
> chp.diamonds <- diamonds[sample(1:nrow(diamonds), size=10000, prob=1-price.norm, replace=TRUE),]
> 
> tp1 <- tableplot(exp.diamonds)
> tp2 <- tableplot(chp.diamonds)
Error in ff(initdata = initdata, length = length, levels = levels, ordered = ordered,  : 
  write error
Calls: tableplot ... tablePrepare -> lapply -> FUN -> clone -> clone.ff -> assign -> ff
Execution halted
Running ‘testthat.R’ [44s/155s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  ── 1. Error: (unknown) (@test_non-latin.R#13)  ─────────────────────────────────
  no field, method or inner class called 'handled' 
  1: test_that("Read French language PDF w/correct encoding", {
         f2 <- "http://www.europarl.europa.eu/oeil/popups/printfichetechnical.pdf?id=673511&lang=fr"
         t2a <- extract_text(f2, page = 1, encoding = "latin1")
         t2b <- extract_text(f2, page = 1, encoding = "UTF-8")
     }) at testthat/test_non-latin.R:13
  2: test_code(desc, code, env = parent.frame())
  3: tryCatch(withCallingHandlers({
         eval(code, test_env)
         if (!handled && !is.null(test)) {
             skip_empty()
         }
     }, expectation = handle_expectation, skip = handle_skip, warning = handle_warning, 
         message = handle_message, error = handle_error), error = handle_fatal, skip = function(e) {
     })
  4: tryCatchList(expr, classes, parentenv, handlers)
  5: tryCatchOne(tryCatchList(expr, names[-nh], parentenv, handlers[-nh]), names[nh], 
         parentenv, handlers[[nh]])
  6: doTryCatch(return(expr), name, parentenv, handler)
  7: tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
  8: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  9: value[[3L]](cond)
  10: isTRUE(e$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: 89 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_non-latin.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    sql   8.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/telefit.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
Package suggested but not available for checking: ‘tesseract’
Package unavailable to check Rd xrefs: ‘tesseract’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.6Mb
Package suggested but not available for checking: ‘Rblpapi’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: nproc:  not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command: 'Illegal seek'
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc         3.9Mb
    rmarkdown   1.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.1.0
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-131 (tmap-getstarted.Rmd) 
Error: processing vignette 'tmap-getstarted.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (toOrdinal.Rmd) 
Error: processing vignette 'toOrdinal.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
File ‘tpr/libs/tpr.so’:
  Found ‘__1cDstdEcerr_’, possibly from ‘std::cerr’ (C++)
    Object: ‘utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    doc       2.8Mb
    extdata   8.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.824,-1.7133&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

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

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



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
there is no package called 'webshot'
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(trustOptim)
  > 
  > test_check("trustOptim")
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    50       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   128       0.000000       0.000000                    Success
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
   287       0.000000       0.000000Radius of trust region is less than stop.trust.radius
  
  ── 1. Failure: Rosenbrock (@test_rosenbrock.R#67)  ─────────────────────────────
  opt0\$status does not match "Success".
  Actual value: "Radius of trust region is less than stop\.trust\.radius"
  
  Beginning optimization
  
  Iteration has terminated
  
  iter            f           nrm_gr                     status
    65       0.000000       0.000000                    Success
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 15 SKIPPED: 0 FAILED: 1
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘tsibble-Ex.R’ failed
The error most likely occurred in:

> ### Name: as_tsibble
> ### Title: Coerce to a tsibble object
> ### Aliases: as_tsibble as.tsibble as_tsibble.tbl_df as_tsibble.tbl_ts
> ###   as_tsibble.data.frame as_tsibble.list as_tsibble.ts as_tsibble.mts
> ###   as_tsibble.msts as_tsibble.hts
> 
> ### ** Examples
> 
> # coerce tibble to tsibble w/o a key ----
> tbl1 <- tibble(
+   date = as.Date("2017-01-01") + 0:9,
+   value = rnorm(10)
+ )
> as_tsibble(tbl1)
Column `date` is the index.
# A tsibble: 10 x 2 [1D]
   date        value
   <date>      <dbl>
 1 2017-01-01 -0.626
 2 2017-01-02  0.184
 3 2017-01-03 -0.836
 4 2017-01-04  1.60 
 5 2017-01-05  0.330
 6 2017-01-06 -0.820
 7 2017-01-07  0.487
 8 2017-01-08  0.738
 9 2017-01-09  0.576
10 2017-01-10 -0.305
> # specify the index var
> as_tsibble(tbl1, index = date)
# A tsibble: 10 x 2 [1D]
   date        value
   <date>      <dbl>
 1 2017-01-01 -0.626
 2 2017-01-02  0.184
 3 2017-01-03 -0.836
 4 2017-01-04  1.60 
 5 2017-01-05  0.330
 6 2017-01-06 -0.820
 7 2017-01-07  0.487
 8 2017-01-08  0.738
 9 2017-01-09  0.576
10 2017-01-10 -0.305
> 
> # coerce tibble to tsibble with one key ----
> # "date" is automatically considered as the index var, and "group" is the key
> tbl2 <- tibble(
+   mth = rep(yearmonth("201701") + 0:9, 3),
+   group = rep(c("x", "y", "z"), each = 10),
+   value = rnorm(30)
+ )
> as_tsibble(tbl2, key = id(group))
Column `mth` is the index.
Error: Column `mth` (the index) must not contain `NA`.
Execution halted
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc         5.5Mb
    dummydata   1.5Mb
    libs        1.9Mb
Error in re-building vignettes:
  ...
Warning 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

Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
there is no package called 'TSstudio'
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: magic
Loading required package: abind

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


Quitting from lines 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/unrtf.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    doc   8.2Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    data  14.9Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    data  29.1Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   6.4Mb
Running examples in ‘utiml-Ex.R’ failed
The error most likely occurred in:

> ### Name: ctrl
> ### Title: CTRL model for multi-label Classification
> ### Aliases: ctrl
> 
> ### ** Examples
> 
> model <- ctrl(toyml, "RANDOM")
Error in ctrl(toyml, "RANDOM") : 
  There are no installed package 'FSelector' to use CTRL multi-label classifier
Execution halted
Running ‘testthat.R’ [19s/24s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  ── 1. Error: CTRL (@test_brclassifiers.R#94)  ──────────────────────────────────
  There are no installed package 'FSelector' to use CTRL multi-label classifier
  1: ctrl(train, "RANDOM") at testthat/test_brclassifiers.R:94
  2: stop(paste("There are no installed package 'FSelector' to use CTRL", "multi-label classifier"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1120 SKIPPED: 21 FAILED: 1
  1. Error: CTRL (@test_brclassifiers.R#94) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Loading required package: randomForest
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.

Attaching package: 'randomForest'

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

    importance

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

    margin

Loading required package: parallel
Quitting from lines 123-126 (varrank.Rmd) 
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
there is no package called 'FSelector'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-36 (intro_to_vegalite.Rmd) 
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    doc    1.3Mb
    help   2.8Mb
installed size is 12.1Mb
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    doc           5.7Mb
    htmlwidgets   4.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-27 (Introduction-to-visNetwork.Rmd) 
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    extdata  11.3Mb
Found the following significant warnings:
  "predict.c", line 111: warning: improper pointer/integer combination: op "<"
See ‘/home/ripley/R/packages/tests32/VLMC.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/wand.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.3Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc  12.3Mb
Package suggested but not available for checking: ‘rcdk’
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    client  10.1Mb
    doc      1.1Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-39 (wordcloud.Rmd) 
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.1Mb
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    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    data  14.3Mb
Package required but not available: ‘x12’

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

> ### Name: JuliaFunction-class
> ### Title: Proxy Objects in R for Julia Functions
> ### Aliases: JuliaFunction JuliaFunction-class
> ###   initialize,JuliaFunction-method
> 
> ### ** Examples
> 
> if(findJulia(test = TRUE)) {
+   set.seed(228)
+   x <- matrix(rnorm(1000),20,5)
+   xm <- juliaSend(x)
+   svdJ <- JuliaFunction("svdfact")
+   sxm <- svdJ(xm)
+   sxm
+ }
sh: no:  not found
Error in base::system(cmd, intern = TRUE) : 
  error in running command: 'Illegal seek'
Calls: findJulia -> testJSON -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 818-843 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
(converted from warning) Removed 4070 rows containing missing values (geom_raster).
Execution halted
Running ‘test-all.R’ [23s/574s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  ── 1. Failure: Expected errors (@testTransformCRS.R#39)  ───────────────────────
  `workflow(...)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/zstdr.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Welcome to package ztable ver 0.2.0
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 103-108 (ztable_update.Rmd) 
Error: processing vignette 'ztable_update.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
In addition: Warning message:
In engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Execution halted
Found the following significant warnings:
  analyzeFMRI.c:948:3: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  analyzeFMRI.c:975:5: warning: ‘strncat’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/AnalyzeFMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  pa.c:247:2: warning: initialization of ‘struct audio_instance * (*)(struct SEXPREC *, float,  int)’ from incompatible pointer type ‘void * (*)(struct SEXPREC *, float,  int)’ [-Wincompatible-pointer-types]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BANOVA.Rcheck/00install.out’ for details.
gimli.990hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  Blasso.cpp:451:53: warning: ‘*<unknown>.Blasso::icept’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Found the following significant warnings:
  mcmc.c:337:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
gimli.1464hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8891hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.17111hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.26440hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.14867hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31846hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23686hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.32717hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8188hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16493hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28086hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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 ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Boom.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/BoomSpikeSlab.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [30s/35s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("broom")
  Loading required package: broom
  ── 1. Error: (unknown) (@test-biglm.R#7)  ──────────────────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(am ~ mpg, mtcars, family = binomial()) at testthat/test-biglm.R:7
  2: bigglm(am ~ mpg, mtcars, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 906 SKIPPED: 2 FAILED: 1
  1. Error: (unknown) (@test-biglm.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.28657hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7fb436e11b40, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Found the following significant warnings:
  catnet_rexport.cpp:202:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:206:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:213:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:216:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:217:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:232:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:231:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/catnet.Rcheck/00install.out’ for details.
gimli.8459hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  guess_type.c:14:9: warning: ‘strncpy’ specified bound 512 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/checkmate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  lprintf.c:336:17: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/creditr.Rcheck/00install.out’ for details.
gimli.16947hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  hash.c:144:5: warning: ‘strncpy’ specified bound 2048 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Found the following significant warnings:
  GetData.c:342:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
  GetData.c:355:15: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size 3 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/DetSel.Rcheck/00install.out’ for details.
Found the following significant warnings:
  clipper.cpp:721:34: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘struct ClipperLib::TEdge’; use assignment or value-initialization instead [-Wclass-memaccess]
  dbfopen.c:1346:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:1328:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopen.c:879:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopen.c:1693:9: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
  dbfopen.c:2065:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dggridR.Rcheck/00install.out’ for details.
gimli.30919hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6745hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.14633hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.22183hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.16265hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.30984hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25052hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.31443hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5820hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.13130hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21853hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [23s/25s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  ── 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ───
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  ── 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ───
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2947 SKIPPED: 3 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Found the following significant warnings:
  main.c:334:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:575:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:518:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:805:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:755:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1034:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:983:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1377:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1279:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1678:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1962:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:1912:13: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2316:7: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
  main.c:2212:17: warning: ‘strncpy’ specified bound 10 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/enviPat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  epanet.c:999:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1000:5: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:1492:3: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2308:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  epanet.c:2309:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:454:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input1.c:455:7: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
  input3.c:604:2: warning: ‘strncpy’ output may be truncated copying 31 bytes from a string of length 31 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Creating package 'fakepack' in '/tmp/RtmpjMnzwR'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
* installing *source* package ‘fakepack’ ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  ‘fakepack’ 
*** installing help indices
** building package indices
** testing if installed package can be loaded
* DONE (fakepack)
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette ‘An_Introduction_to_fakemake.Rmd’ failed with diagnostics:
there is no package called 'spelling'
Execution halted
Found the following significant warnings:
  Rconnection.h:202:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.h:205:12: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
  Rconnection.cc:53:20: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
  Warning: 'cBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Examples with CPU or elapsed time > 5s
     user system elapsed
fcr 8.095  0.083   8.382
Found the following significant warnings:
  FLAN_Clone.h:131:11: warning: ‘*<unknown>.FLAN_SimClone::mDist’ is used uninitialized in this function [-Wuninitialized]
  FLAN_Clone.h:204:11: warning: ‘*<unknown>.FLAN_SimInhomogeneousClone::mMU’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/flan.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:275:7: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/freeknotsplines.Rcheck/00install.out’ for details.
Found the following significant warnings:
  hap_c.c:380:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  hap_c.c:392:28: warning: ‘%03d’ directive writing between 3 and 10 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gap.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Gdmlib.cpp:2352:19: warning: ‘%lf’ directive writing between 3 and 317 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/geometry.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [28s/40s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getTBinR)
  > 
  > test_check("getTBinR")
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=estimates'
  downloaded 711 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=dictionary'
  downloaded 63 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=estimates'
  downloaded 711 KB
  
  trying URL 'https://extranet.who.int/tme/generateCSV.asp?ds=mdr_rr_estimates'
  downloaded 30 KB
  
  ── 1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_b
  plot$labels$fill not equal to `test_label`.
  1/1 mismatches
  x[1]: "`test (test - test)`"
  y[1]: "test (test - test)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 83 SKIPPED: 29 FAILED: 1
  1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_burden.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Found the following significant warnings:
  dump_json_ast.cpp:21:12: warning: ‘char* strncpy(char*, const char*, size_t)’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/graphql.Rcheck/00install.out’ for details.
gimli.4705hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  readstat/readstat_writer.c:82:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/readstat_writer.c:261:5: warning: ‘strncpy’ specified bound 256 equals destination size [-Wstringop-truncation]
  readstat/readstat_writer.c:316:9: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  readstat/sas/readstat_sas7bcat_write.c:108:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:284:5: warning: ‘strncpy’ output may be truncated copying 64 bytes from a string of length 99 [-Wstringop-truncation]
  readstat/sas/readstat_sas.c:337:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 31 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:150:5: warning: ‘strncpy’ output may be truncated copying 9 bytes from a string of length 9 [-Wstringop-truncation]
  readstat/spss/readstat_sav_write.c:158:5: warning: ‘strncpy’ output may be truncated copying 8 bytes from a string of length 8 [-Wstringop-truncation]
  readstat/spss/readstat_por_write.c:194:5: warning: ‘strncpy’ output truncated before terminating nul copying 20 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/haven.Rcheck/00install.out’ for details.
Found the following significant warnings:
  gener.c:39:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(stringr)
  > library(io)
  Loading required package: filenamer
  > 
  > test_check("io")
  ── 1. Error: (unknown) (@test_read-write-read.R#8)  ────────────────────────────
  no applicable method for 'h5write' applied to an object of class "character"
  1: test_read_write_read(f) at testthat/test_read-write-read.R:8
  2: qwrite(x, outfile) at /home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/io.Rcheck/tests/testthat/helper.R:48
  3: .qwrite(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  4: qwrite.hdf5(x, if (is.filename(file)) as.character(file) else file, if (is.null(type)) .infer_file_type(file) else type, 
         ...)
  5: .write_hdf5_array(x, file)
  6: rhdf5::h5write("array", file, "type")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [0m/17m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 27/10/2018"
  ── 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ────────────────────────
  Recv failure: Connection timed out
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.18402hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  push_parser.c:75:5: warning: ‘strncpy’ specified bound 1024 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/jsonlite.Rcheck/00install.out’ for details.
gimli.8483hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16319hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.27005hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.3904hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.6317hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18500hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16004hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.26893hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.3342hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10807hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.19072hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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 ‘testthat.R’ [18s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > if (packageVersion("testthat") >= "0.7.1.99") {
  +   library(testthat)  
  +   test_check("lubridate")
  + }
  Loading required package: lubridate
  
  Attaching package: 'lubridate'
  
  The following object is masked from 'package:base':
  
      date
  
  ── 1. Failure: difftime comparison with periods works (@test-ops-compare.R#63)  
  days(1) == (t + days(1)) - t isn't true.
  
  ── 2. Failure: difftime comparison with periods works (@test-ops-compare.R#64)  
  (t + days(1)) - t == days(1) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 2451 SKIPPED: 4 FAILED: 2
  1. Failure: difftime comparison with periods works (@test-ops-compare.R#63) 
  2. Failure: difftime comparison with periods works (@test-ops-compare.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  liblwgeom/lwutil.c:317:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:323:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:344:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
  liblwgeom/lwutil.c:349:5: warning: ‘strncat’ specified bound 3 equals source length [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/lwgeom.Rcheck/00install.out’ for details.
gimli.29561hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2335hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.8152hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.14779hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.7362hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.15134hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.23780hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1066hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11222hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  migrate.c:179:30: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:186:26: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:199:28: warning: ‘.asc’ directive writing 4 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:286:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:312:29: warning: ‘%d’ directive writing between 1 and 8 bytes into a region of size between 1 and 128 [-Wformat-overflow=]
  migrate.c:559:31: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:595:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
  migrate.c:603:27: warning: ‘%s’ directive writing up to 127 bytes into a region of size between 0 and 127 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
gimli.5647hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  monetdblite/src/gdk/gdk_heap.c:189:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  monetdblite/src/gdk/gdk_heap.c:260:30: warning: ‘%s’ directive writing likely 3 or more bytes into a region of size between 0 and 99 [-Wformat-overflow=]
  monetdblite/src/mal/sqlbackend/rel_bin.c:2949:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/rel_bin.c:1083:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3193:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3196:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/mal/sqlbackend/sql_statement.c:3186:3: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_planner.c:82:4: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_semantic.c:54:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  monetdblite/src/sql/server/rel_updates.c:1729:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/MonetDBLite.Rcheck/00install.out’ for details.
gimli.3605hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  medusa.long2text.cpp:16:21: warning: ‘%ld’ directive writing between 1 and 20 bytes into a region of size 16 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Numero.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Quitting from lines 72-74 (OECD.Rmd) 
Error: processing vignette ‘OECD.Rmd’ failed with diagnostics:
GnuTLS recv error (-54): Error in the pull function.
Execution halted
gimli.31766hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running ‘exporting-methods.R’ [3s/3s]
  Running ‘mahal-dist.R’ [3s/3s]
  Running ‘testthat.R’ [21s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(optmatch)
  Loading required package: survival
  The optmatch package has an academic license. Enter relaxinfo() for more information.
  > 
  > test_check("optmatch")
  ── 1. Error: Bigglm distances (@test.match_on.R#298)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.match_on.R:298
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ── 2. Error: scores with bigglm (@test.scores.R#222)  ──────────────────────────
  no applicable method for 'bigglm' applied to an object of class "data.frame"
  1: bigglm(Z ~ X1 + X2, data = test.data, family = binomial()) at testthat/test.scores.R:222
  2: bigglm(Z ~ X1 + X2, data = test.data, family = binomial())
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1308 SKIPPED: 0 FAILED: 2
  1. Error: Bigglm distances (@test.match_on.R#298) 
  2. Error: scores with bigglm (@test.scores.R#222) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.3333hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.22643hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running ‘testthat.R’ [11s/36s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pavo)
  > 
  > test_check("pavo")
  ── 1. Error: classify (@test-images.R#79)  ─────────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = fake_IDs) at testthat/test-images.R:79
  
  ── 2. Error: adjacency (@test-images.R#156)  ───────────────────────────────────
  attempt to set an attribute on NULL
  1: classify(imgfakes, kcols = 2) at testthat/test-images.R:156
  
  Read 10820 items
  Read 18823 items
  Read 10824 items
  Read 10820 items
  Read 18823 items
  Read 10824 items
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 143 SKIPPED: 0 FAILED: 2
  1. Error: classify (@test-images.R#79) 
  2. Error: adjacency (@test-images.R#156) 
  
  Error: testthat unit tests failed
  Execution halted
gimli.21037hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28510hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.3667hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.10189hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.31811hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16433hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7414hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.14914hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.25514hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31378hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5454hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.21544hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29230hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.4068hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.10733hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.32525hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16888hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.8835hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.16592hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27321hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32616hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6560hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.23578hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.32456hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.

Found the following apparent S3 methods exported but not registered:
  cbind.ddmatrix rbind.ddmatrix
See section ‘Registering S3 methods’ in the ‘Writing R Extensions’
manual.
gimli.4850hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.11930hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.5045hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.18653hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.14816hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.25463hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.31477hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5521hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.10952hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
S3 methods shown with full name in documentation object 'binds':
  ‘rbind.ddmatrix’ ‘cbind.ddmatrix’

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.
gimli.21296hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28699hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.3735hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.10234hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.973hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.16572hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.12181hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.20404hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29547hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2419hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7853hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.12059hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.27615hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2956hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.9359hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.15040hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.2322hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.20785hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.12305hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.20416hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.29534hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.2361hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.7772hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
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.
gimli.28320hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Running ‘testthat.R’ [231s/343s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(peakPantheR)
  
  This is peakPantheR version 1.2.0 
  
  > 
  > test_check("peakPantheR")
  ── 1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180)  ────
  unused arguments (limits, n)
  1: evaluate_promise(annotationDiagnosticMultiplot(input_plots)) at testthat/test_annotationDiagnosticMultiplot.R:180
  2: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  3: force(code)
  4: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  5: withVisible(code)
  6: annotationDiagnosticMultiplot(input_plots)
  7: ggplot2::layer_scales(tmp_rtPeakwidthVert)
  8: ggplot_build(plot)
  9: ggplot_build.ggplot(plot)
  10: layout$setup_panel_params()
  ...
  16: f(..., self = self)
  17: parent$setup_panel_params(scale_x, scale_y, params)
  18: f(..., self = self)
  19: train_cartesian(scale_x, self$limits$x, "x")
  20: scale$break_info(range)
  21: f(..., self = self)
  22: ggproto_parent(ScaleContinuous, self)$break_info(range)
  23: f(..., self = self)
  24: self$get_breaks_minor(b = major, limits = range)
  25: f(..., self = self)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1147 SKIPPED: 0 FAILED: 1
  1. Error: default multiplot (@test_annotationDiagnosticMultiplot.R#180) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  fdouble_metaphone.c:268:5: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PGRdup.Rcheck/00install.out’ for details.
gimli.16144hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.21365hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.28898hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.4474hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.4119hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.12886hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11106hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.18015hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.26435hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1170hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.9974hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 2 equals destination size [-Wstringop-truncation]
  zhegv.c:216:27: warning: ‘strncpy’ specified bound 3 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/PRIMME.Rcheck/00install.out’ for details.
Found the following significant warnings:
  R4dfp-object.c:253:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
  R4dfp-object.c:260:3: warning: ‘strncpy’ output truncated before terminating nul copying 9 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  kleinkram.cc:1018:18: warning: ‘ '’ directive writing 2 bytes into a region of size between 1 and 1000 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RandomFieldsUtils.Rcheck/00install.out’ for details.
Found the following significant warnings:
  avc_binwr.c:166:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:173:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:180:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:187:9: warning: ‘strncpy’ output truncated before terminating nul copying 3 bytes from a string of the same length [-Wstringop-truncation]
  avc_binwr.c:1453:29: warning: ‘%4.4d’ directive writing between 4 and 10 bytes into a region of size 5 [-Wformat-overflow=]
  avc_binwr.c:1553:28: warning: ‘%s’ directive writing up to 39 bytes into a region of size between 38 and 77 [-Wformat-overflow=]
  avc_e00write.c:386:30: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  avc_e00write.c:387:30: warning: ‘-ID’ directive writing 3 bytes into a region of size between 1 and 40 [-Wformat-overflow=]
  avc_e00write.c:401:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:397:61: warning: ‘%s’ directive writing up to 39 bytes into a region of size 17 [-Wformat-overflow=]
  avc_e00write.c:409:39: warning: ‘%s’ directive writing up to 39 bytes into a region of size 33 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  samtools/bam.c:118:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  samtools/razf.c:178:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
  rbamtools.cpp:126:10: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rbamtools.Rcheck/00install.out’ for details.
Running examples in ‘Rchoice-Ex.R’ failed
The error most likely occurred in:

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

Model: binomial
Model estimated on: Sat Oct 27 06:47:27 AM 2018 

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


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

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

Optimization of log-likelihood by Newton-Raphson maximisation
Log Likelihood: -452.7
Number of observations: 753
Number of iterations: 4
Exit of MLE: gradient close to zero> 
> library(sandwich)
> estfun(probit) 
Error in UseMethod("estfun") : 
  no applicable method for 'estfun' applied to an object of class "Rchoice"
Calls: estfun
Execution halted
Found the following significant warnings:
  Rreadsdpa.c:608:15: warning: ‘strncpy’ output may be truncated copying 3999 bytes from a string of length 3999 [-Wstringop-truncation]
  Rreadsdpa.c:1041:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  Rreadsdpa.c:1042:13: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:164:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
  dsdpsetoptions.c:165:4: warning: ‘strncpy’ output may be truncated copying 39 bytes from a string of length 39 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rdsdp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  compile.cc:292:69: warning: ‘void* memset(void*, int, size_t)’ clearing an object of non-trivial type ‘class re2::Prog::Inst’; use assignment or value-initialization instead [-Wclass-memaccess]
  regexp.cc:343:33: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
  regexp.cc:344:32: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘class re2::Regexp’ with no trivial copy-assignment [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Found the following significant warnings:
  localtime.c:1817:5: warning: ‘strncpy’ specified bound 1000 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/readr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  phonet.c:1207:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  phonet.c:1208:34: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RecordLinkage.Rcheck/00install.out’ for details.
gimli.19783hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.24385hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.981hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.14113hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.23748hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.24093hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1730hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6303hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.13512hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.24531hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.1951hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.9952hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  RhpcMPI.c:301:5: warning: ‘strncpy’ specified bound 4096 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  cornellout.cpp:99:20: warning: ‘%2d’ directive writing between 2 and 11 bytes into a region of size between 0 and 931 [-Wformat-overflow=]
  cornellout.cpp:137:26: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  cornellout.cpp:129:26: warning: ‘%s’ directive writing up to 999 bytes into a region of size between 988 and 995 [-Wformat-overflow=]
  mat.cpp:315:4: warning: ‘*<unknown>.dataMat::p’ is used uninitialized in this function [-Wuninitialized]
  tilia.cpp:179:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 61 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:180:10: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 19 bytes from a string of length 19 [-Wstringop-truncation]
  tilia.cpp:225:14: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 199 [-Wstringop-truncation]
  tilia.cpp:228:17: warning: ‘char* strncpy(char*, const char*, size_t)’ output may be truncated copying 8 bytes from a string of length 29 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rioja.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/rJava/libs/rJava.so’:
  Found ‘_exit’, possibly from ‘_exit’ (C)
  Found ‘stderr’, possibly from ‘stderr’ (C)
  Found ‘stdout’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CStackStart’,
    ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: ‘json_shared_string::len’ will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   ‘json_shared_string::json_shared_string_internal* json_shared_string::_str’ [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: ‘JSONStream::state’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   ‘void (* JSONStream::call)(void*, void*)’ [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: ‘JSONStream::err_call’ will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   ‘json_string JSONStream::buffer’ [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: ‘internalJSONNode::_name_encoded’ will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   ‘json_string internalJSONNode::_name’ [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RJSONIO.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rlecuyer.Rcheck/00install.out’ for details.
Found the following significant warnings:
  origcmaes.cc:2852:13: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2855:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
  origcmaes.cc:2858:12: warning: ‘char* strncat(char*, const char*, size_t)’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rmalschains.Rcheck/00install.out’ for details.
gimli.10353hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.17388hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
gimli.28704hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
gimli.3452hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
gimli.7279hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11839hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.15141hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
gimli.23258hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.28851hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.5046hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.11524hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Copyright (c) 2015-present, Facebook, Inc.
  > # All rights reserved.
  > #
  > # This source code is licensed under the BSD-style license found in the
  > # LICENSE file in the root directory of this source tree. An additional grant
  > # of patent rights can be found in the PATENTS file in the same directory.
  > 
  > library("testthat")
  > library("DBI")
  > library("RPresto")
  > 
  > test_check("RPresto")
  -- 1. Failure: as() works (@test-translate_sql.R#22)  --------------------------
  translate_sql(as(x, 0), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DOUBLE)").
  1/1 mismatches
  x[1]: "AS(\"x\", 0.0)"
  y[1]: "CAST(\"x\" AS DOUBLE)"
  
  -- 2. Failure: as() works (@test-translate_sql.R#26)  --------------------------
  translate_sql(pmax(x), con = s[["con"]]) not equal to dplyr::sql("GREATEST(\"x\")").
  1/1 mismatches
  x[1]: "MAX(\"x\")"
  y[1]: "GREATEST(\"x\")"
  
  -- 3. Failure: as() works (@test-translate_sql.R#30)  --------------------------
  translate_sql_(...) not equal to dplyr::sql("CAST(\"x\" AS ARRAY<VARCHAR>)").
  1/1 mismatches
  x[1]: "AS(\"x\", ())"
  y[1]: "CAST(\"x\" AS ARRAY<VARCHAR>)"
  
  -- 4. Failure: as() works (@test-translate_sql.R#39)  --------------------------
  translate_sql_(list(substituted.expression), con = s[["con"]]) not equal to dplyr::sql("CAST(\"x\" AS DATE)").
  1/1 mismatches
  x[1]: "AS(\"x\", '2018-10-27')"
  y[1]: "CAST(\"x\" AS DATE)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 276 SKIPPED: 28 FAILED: 4
  1. Failure: as() works (@test-translate_sql.R#22) 
  2. Failure: as() works (@test-translate_sql.R#26) 
  3. Failure: as() works (@test-translate_sql.R#30) 
  4. Failure: as() works (@test-translate_sql.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/Rserve/libs/Rserve.so’:
  Found ‘exit’, possibly from ‘exit’ (C)
  Found ‘rand’, possibly from ‘rand’ (C)
  Found ‘random’, possibly from ‘random’ (C)
  Found ‘srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  RngStreams.c:332:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rstream.Rcheck/00install.out’ for details.
Found the following significant warnings:
  bgc_hmm.c:241:31: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 10000 [-Wformat-overflow=]
  rph_tfbs.c:371:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:351:11: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  rph_tfbs.c:819:5: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Found the following significant warnings:
  geometry/s2loop.cc:85:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2loop.cc:247:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:52:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2polyline.cc:94:73: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘S2Point’ {aka ‘class Vector3<double>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  geometry/s2regioncoverer.cc:119:28: warning: ‘void* memset(void*, int, size_t)’ clearing an object of type ‘struct S2RegionCoverer::Candidate’ with no trivial copy-assignment; use assignment or value-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/s2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mmb.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/scio.Rcheck/00install.out’ for details.
Found the following significant warnings:
  catnet_rexport.cpp:221:17: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:229:15: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:237:16: warning: ‘%d’ directive writing between 1 and 10 bytes into a region of size between 0 and 1023 [-Wformat-overflow=]
  catnet_rexport.cpp:240:18: warning: ‘%d’ directive writing between 1 and 11 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
  catnet_rexport.cpp:241:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:258:17: warning: ‘sprintf’ may write a terminating nul past the end of the destination [-Wformat-overflow=]
  catnet_rexport.cpp:257:18: warning: ‘, ’ directive writing 2 bytes into a region of size between 1 and 1024 [-Wformat-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_1_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
gimli.22511hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
gimli.6939hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/spectrolab.Rcheck/00install.out’ for details.
gimli.1644hfi_wait_for_device: The /dev/hfi1_0 device failed to appear after 15.0 seconds: Connection timed out
Found the following significant warnings:
  dbfopenSSN.c:1119:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:1100:6: warning: ‘strncpy’ output may be truncated copying between 0 and 399 bytes from a string of length 399 [-Wstringop-truncation]
  dbfopenSSN.c:663:2: warning: ‘strncpy’ output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
  dbfopenSSN.c:1511:2: warning: ‘strncpy’ output may be truncated copying 11 bytes from a string of length 11 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, int>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/sparsepp/include/sparsepp/spp_utils.h:422:44: warning: ‘void* realloc(void*, size_t)’ moving an object of non-trivially copyable type ‘struct std::pair<const std::pair<unsigned int, unsigned int>, float>’; use ‘new’ and ‘delete’ instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Found the following significant warnings:
  RngStream.c:347:4: warning: ‘strncpy’ specified bound depends on the length of the source argument [-Wstringop-overflow=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TPmsm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libqhull/rboxlib.c:351:5: warning: ‘strncat’ output may be truncated copying between 0 and 199 bytes from a string of length 199 [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: replacing previous import ‘gdalUtils::gdal_rasterize’ by ‘sf::gdal_rasterize’ when loading ‘uavRmp’
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/uavRmp.Rcheck/00install.out’ for details.
Found the following significant warnings:
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<> >::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::MemoryPoolAllocator<> >’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<> >’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  include/rapidjson/document.h:1952:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>::Member’ {aka ‘struct rapidjson::GenericMember<rapidjson::UTF8<>, rapidjson::CrtAllocator>’} with no trivial copy-assignment; use copy-assignment instead [-Wclass-memaccess]
  include/rapidjson/document.h:1939:24: warning: ‘void* memcpy(void*, const void*, size_t)’ writing to an object of type ‘class rapidjson::GenericValue<rapidjson::UTF8<>, rapidjson::CrtAllocator>’ with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/validatejsonr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  tabix/razf.c:188:2: warning: ‘strncpy’ output truncated before terminating nul copying 4 bytes from a string of the same length [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Found the following significant warnings:
  libxlsxwriter/xmlwriter.c:156:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:160:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:164:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:168:17: warning: ‘strncat’ specified bound 6 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:198:17: warning: ‘strncat’ specified bound 5 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:202:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  libxlsxwriter/xmlwriter.c:206:17: warning: ‘strncat’ specified bound 4 equals source length [-Wstringop-overflow=]
  tmpfileplus/tmpfileplus.c:172:3: warning: ‘strncpy’ specified bound 4097 equals destination size [-Wstringop-truncation]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/writexl.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [18s/32s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  ── 1. Failure: Expected errors (@testTransformCRS.R#39)  ───────────────────────
  `workflow(...)` did not throw an error.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ABHgenotypeR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ACSNMineR.Rcheck/00install.out' for details.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R  13.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ACTCD.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'Matrix' 'coda' 'mvtnorm' 'MCMCpack' 'spatstat' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/afex.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/AFM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/AID.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AmpliconDuo.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ANOM.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.2Mb
    help   1.1Mb
Packages suggested but not available for checking:
  'sfit' 'expectile' 'HaarSeg' 'mpcbs'
Packages suggested but not available for checking: 'REBayes' 'Rmosek'
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(devtools)
  > library(assertive.data)
  > 
  > with_envvar(
  +   c(LANG = "en_US"),
  +   test_check("assertive.data")
  + )
  Error in with_envvar(c(LANG = "en_US"), test_check("assertive.data")) : 
    could not find function "with_envvar"
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/audio.Rcheck/00install.out' for details.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BACA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/bamdit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BANOVA.Rcheck/00install.out' for details.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'bcmaps.rdata' 'doMC'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/beanz.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/bfast.Rcheck/00install.out' for details.
installed size is 142.0Mb
  sub-directories of 1Mb or more:
    include  141.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/BIGL.Rcheck/00install.out' for details.
Package which this enhances but not available for checking: 'synchronicity'
Package unavailable to check Rd xrefs: 'synchronicity'
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.6Mb
Depends: includes the non-default packages:
  'colorspace' 'deldir' 'rgl' 'tcltk' 'tcltk2' 'tkrplot'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/BNSP.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/C443.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/CAinterprTools.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/camtrapR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/cancerGI.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R        1.0Mb
    data     1.5Mb
    models   2.4Mb
Package required but not available: 'OpenCL'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/CAvariants.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/CensMixReg.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ChainLadder.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ClusterR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Compind.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Running examples in 'ctsem-Ex.R' failed
The error most likely occurred in:

> ### Name: ctStanParMatrices
> ### Title: Returns model equation and other matrices from a ctStanFit
> ###   object, and vector of values for free parameters.
> ### Aliases: ctStanParMatrices
> 
> ### ** Examples
> 
> ctStanParMatrices(ctstantestfit,rep(0,17))
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cudaBayesreg.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'xtable' 'akima' 'R.oo' 'R.methodsS3' 'matlab' 'lattice' 'locfit'
  'grid'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running 'testthat.R' [48s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > test_check("DeclareDesign")
  -- 1. Failure: error if you try to draw POs at a level using a variable that doe
  `my_potential_outcomes_formula(pop)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 436 SKIPPED: 1 FAILED: 1
  1. Failure: error if you try to draw POs at a level using a variable that doesn't exist at that level (@test-potential-outcomes.R#160) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerExtras.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerPlugInExample.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'Deducer' 'psych' 'GPArotation' 'mvnormtest' 'irr' 'klaR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Deducer.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'JavaGD' 'Deducer' 'sp' 'maptools' 'OpenStreetMap' 'scales' 'rgdal'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerSpatial.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerSurvival.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DeducerText.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/demu.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/dendrometeR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DengueRT.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex' 'Rmosek'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/DGCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/diveRsity.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'gurobi' 'Rmosek'
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ---
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  -- 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ---
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  == testthat results  ===========================================================
  OK: 2939 SKIPPED: 6 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ---
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  -- 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ---
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  == testthat results  ===========================================================
  OK: 2939 SKIPPED: 6 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   3.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/drugCombo.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs   4.3Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(earthtones)
  > 
  > test_check("earthtones")
  -- 1. Error: returns normal (@test-earth.R#5)  ---------------------------------
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.759,-125.673&zoom=11&size=640x640&scale=2&maptype=satellite&language=en-EN&sensor=false'
  1: expect_is(get_earthtones(), "palette") at testthat/test-earth.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: get_earthtones()
  5: ggmap::get_map(location = c(longitude, latitude), maptype = "satellite", zoom = zoom, 
         ...)
  6: get_googlemap(center = location, zoom = zoom, maptype = maptype, scale = scale, messaging = messaging, 
         urlonly = urlonly, force = force, filename = filename, color = color, language = language)
  7: download.file(url, destfile = tmp, quiet = !messaging, mode = "wb")
  
  == testthat results  ===========================================================
  OK: 3 SKIPPED: 0 FAILED: 1
  1. Error: returns normal (@test-earth.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/elasticIsing.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/emdi.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/envalysis.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/EstimateGroupNetwork.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: xml2
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ft2020_rk310.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 4490 bytes
==================================================
downloaded 4490 bytes

Table t2020_rk310 cached at D:\temp\RtmpCCL3AW/eurostat/t2020_rk310_num_code_TF.rds

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13630 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at D:\temp\RtmpCCL3AW/eurostat/ten00081_date_code_TF.rds
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 5998 bytes
==================================================
downloaded 5998 bytes

Quitting from lines 435-447 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
no applicable method for 'xmlAttrs' applied to an object of class "NULL"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/expsmooth.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ez.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Creating package 'fakepack' in 'D:/temp/RtmpqUzSkJ'
No DESCRIPTION found. Creating with values:


Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
/usr/bin/tar: Record size = 12 blocks
* installing *source* package 'fakepack' ...
** R
** byte-compile and prepare package for lazy loading
** help
No man pages found in package  'fakepack' 
*** installing help indices
** building package indices
** testing if installed package can be loaded
*** arch - i386
*** arch - x64
* DONE (fakepack)
In R CMD INSTALL
/cygdrive/d/Compiler/bin/tar: Record size = 13 blocks
Prerequisite R/throw.R found.
Prerequisite R/throw.R found.
Prerequisite DESCRIPTION found.
Prerequisite R/throw.R found.
Error: processing vignette 'An_Introduction_to_fakemake.Rmd' failed with diagnostics:
there is no package called 'spelling'
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/fDMA.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpYpA6qT\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(feather)
  > 
  > test_check("feather")
  -- 1. Error: can read/write with utf-8 filename (@test-read.R#19)  -------------
  IO error: Failed to open file: D:\temp\RtmpagxP8y\Ã¥.feather
  1: read_feather(path) at testthat/test-read.R:19
  2: feather(path)
  3: openFeather(path)
  
  == testthat results  ===========================================================
  OK: 50 SKIPPED: 0 FAILED: 1
  1. Error: can read/write with utf-8 filename (@test-read.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'fedreporter-Ex.R' failed
The error most likely occurred in:

> ### Name: fe_projects_search
> ### Title: Search Federal RePORTER Projects
> ### Aliases: fe_projects_search
> 
> ### ** Examples
> 
> res = fe_projects_search(
+ project_number = "USFS*",
+ fiscal_year = 2012)
GET command is:
Response [https://api.federalreporter.nih.gov/v1/Projects/search?query=projectNumber%3AUSFS*%24fy%3A2012&offset=1&limit=50]
  Date: 2018-10-26 05:22
  Status: 500
  Content-Type: <unknown>
<EMPTY BODY>
Error in fe_projects_search(project_number = "USFS*", fiscal_year = 2012) : 
  Internal Server Error (HTTP 500).
Calls: fe_projects_search -> <Anonymous>
Execution halted
Depends: includes the non-default packages:
  'gWidgets' 'tcltk' 'tkrplot' 'RGtk2' 'gWidgetsRGtk2' 'cairoDevice'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages suggested but not available for checking: 'doMC' 'RSvgDevice'
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/fma.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ForecastComb.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/forecastHybrid.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/forecast.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/forecTheta.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ftsa.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/fullfact.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc       1.8Mb
    extdata   1.5Mb
    libs      1.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/gastempt.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GeomComb.Rcheck/00install.out' for details.
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(getTBinR)
  > 
  > test_check("getTBinR")
  -- 1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_b
  plot$labels$fill not equal to `test_label`.
  1/1 mismatches
  x[1]: "`test (test - test)`"
  y[1]: "test (test - test)"
  
  == testthat results  ===========================================================
  OK: 75 SKIPPED: 29 FAILED: 1
  1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_burden.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggrasp.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/gimme.Rcheck/00install.out' for details.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GmAMisc.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/GOGANPA.Rcheck/00install.out' for details.
Warning: no function found corresponding to methods exports from 'gpclib' for: 'coerce', 'show'

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

Probably some imports need to be declared in the NAMESPACE file.
read.polyfile: no visible global function definition for 'as'
write.polyfile: no visible global function definition for 'is'
write.polyfile: no visible global function definition for 'as'
[,gpc.poly: no visible global function definition for 'new'
append.poly,gpc.poly-gpc.poly: no visible global function definition
  for 'new'
coerce,data.frame-gpc.poly: no visible global function definition for
  'as'
coerce,list-gpc.poly: no visible global function definition for 'as'
coerce,matrix-gpc.poly: no visible global function definition for 'new'
coerce,numeric-gpc.poly: no visible global function definition for
  'new'
coerce,numeric-gpc.poly.nohole: no visible global function definition
  for 'new'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'as'
intersect,gpc.poly-gpc.poly: no visible global function definition for
  'new'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'as'
setdiff,gpc.poly-gpc.poly: no visible global function definition for
  'new'
tristrip,gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for 'as'
union,gpc.poly-gpc.poly: no visible global function definition for
  'new'
Undefined global functions or variables:
  as is new
Consider adding
  importFrom("methods", "as", "is", "new")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'bug1.R' [1s]
  Running 'reg-tests.R' [1s]
  Comparing 'reg-tests.Rout' to 'reg-tests.Rout.save' ...58c58
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
68c68
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
83c83
< Formal class 'gpc.poly' [package "gpclib"] with 1 slot
---
> Formal class 'gpc.poly' [package "gpclib"] with 1 slots
Running the tests in 'tests/bug1.R' failed.
Complete output:
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gpuR.Rcheck/00install.out' for details.
installed size is 25.7Mb
  sub-directories of 1Mb or more:
    R  25.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GraphPCA.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'taxstats' 'taxstats1516'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/GSIF.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

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

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/htmlwidgets.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/hydroPSO.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'lattice' 'caTools' 'gdata' 'gtools' 'gplots' 'parallel'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/IFP.Rcheck/00install.out' for details.
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    extdata   1.0Mb
    include   2.8Mb
    libs     12.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/IntClust.Rcheck/00install.out' for details.
Running 'testthat.R' [71s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 26/10/2018"
  -- 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ------------------------
  Recv failure: Connection was reset
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/IsingFit.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/itemanalysis.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'partitions' 'VGAM' 'MASS' 'ape' 'apTreeshape' 'geiger' 'gtools'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/jackstraw.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/jmv.Rcheck/00install.out' for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R   7.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/lfl.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Depends: includes the non-default packages:
  'sn' 'moments' 'BB' 'Bolstad2' 'optimx' 'Rmpfr'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   1.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Mcomp.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'lattice' 'locfit' 'maptools' 'quantreg' 'RANN' 'SparseM'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'MASS' 'boot' 'RColorBrewer' 'scatterplot3d' 'tcltk' 'tcltk2'
  'tkrplot' 'rpanel' 'rgl'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'seqinr' 'pcaMethods' 'Matrix' 'ROCR' 'Hmisc' 'KernSmooth' 'seqLogo'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   2.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
Packages suggested but not available for checking: 'doMC' 'doSMP'
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.0Mb
    libs   3.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/mgm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/midasr.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'amap' 'clValid' 'cluster' 'fpc' 'mzR' 'xcms'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Depends: includes the non-default packages:
  'car' 'pdist' 'pls' 'gplots' 'mvtnorm' 'robustbase' 'gtools' 'bitops'
  'caTools' 'pcaPP' 'rrcov'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/mvdalab.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/nearfar.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/NeatMap.Rcheck/00install.out' for details.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         6.5Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/nnfor.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'lpSolve' 'gdata' 'Hmisc' 'rms' 'geometry' 'psych' 'pwt'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Error in re-building vignettes:
  ...
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.1/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See 'd:/Rcompile/CRANpkg/local/3.5/npde.Rcheck/00install.out' for details.
Information on the location(s) of code generating the 'Note's can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to 'yes'.
Packages in Depends field not imported from:
  'mclust' 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/npIntFactRep.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'R.methodsS3' 'MASS' 'matrixStats' 'R.oo' 'R.utils' 'aroma.core'
  'aroma.affymetrix' 'DNAcopy'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/odpc.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/onewaytests.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/OpenCL.Rcheck/00install.out' for details.
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    R        2.4Mb
    libs     6.4Mb
    models   4.7Mb
Package required but not available: 'ROracle'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/partialCI.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'svmpath' 'kernlab' 'affy' 'Biobase' 'ROCR' 'igraph' 'lpSolve'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: decompose_path handles paths with a unicode directory name. (@tes
  actual$dirname not equal to expected$dirname.
  1/1 mismatches
  x[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/CRAN"
  
  -- 2. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.5/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 186 SKIPPED: 18 FAILED: 2
  1. Failure: decompose_path handles paths with a unicode directory name. (@test_decompose_path.R#466) 
  2. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    lib    5.6Mb
    libs   4.6Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/pequod.Rcheck/00install.out' for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      4.4Mb
    data   3.1Mb
Found the following significant warnings:
  Warning: S3 method 'format.SQLiteConnection' was declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/pkgmaker.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'RGtk2' 'gWidgetsRGtk2' 'cairoDevice' 'lattice' 'rggobi' 'ggplot2'
  'proto'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/PlasmaMutationDetector.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/pompom.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/portes.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/predictionInterval.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(processanimateR)
  > 
  > test_check("processanimateR")
  -- 1. Failure: patients example works (@test-issue-4-order.R#6)  ---------------
  `animate_process(patients)` produced warnings.
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Failure: patients example works (@test-issue-4-order.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/prophet.Rcheck/00install.out' for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/qgraph.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/qha.Rcheck/00install.out' for details.
Package required but not available: 'qtbase'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
Packages suggested but not available for checking: 'rcom' 'RDCOMClient'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   2.8Mb
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: RANN
Loading required package: PBSmapping

-----------------------------------------------------------
PBS Mapping 2.70.5 -- Copyright (C) 2003-2018 Fisheries and Oceans Canada

PBS Mapping comes with ABSOLUTELY NO WARRANTY;
for details see the file COPYING.
This is free software, and you are welcome to redistribute
it under certain conditions, as outlined in the above file.

A complete user guide 'PBSmapping-UG.pdf' is located at 
D:/temp/RtmpkPCMFl/RLIBS_1d1c87785465f/PBSmapping/doc/PBSmapping-UG.pdf

Packaged on 2018-06-05
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
https://github.com/pbs-software

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true': HTTP status was '403 Forbidden'

Error: processing vignette 'RapidPolygonLookup.Rnw' failed with diagnostics:
 chunk 1 
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true'
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrMisc.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'biclust' 'fabia' 'iBBiG' 'superbiclust' 'BcDiag' 'rqubic' 'BicARE'
  's4vd' 'BiBitR'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.EACSPIR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.FuzzyClust.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.KMggplot2.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RcmdrPlugin.MA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Rcmdr.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rcplex.Rcheck/00install.out' for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   2.6Mb
Package required but not available: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/replicationInterval.Rcheck/00install.out' for details.
Running 'testthat.R' [4s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(reqres)
  > 
  > test_check("reqres")
  -- 1. Failure: request gets created correctly (@test-request.R#33)  ------------
  req$root is not null.
  
  == testthat results  ===========================================================
  OK: 100 SKIPPED: 0 FAILED: 1
  1. Failure: request gets created correctly (@test-request.R#33) 
  
  Error: testthat unit tests failed
  Execution halted
S3 methods shown with full name in documentation object 'all.vars.character':
  'all.vars.character'

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter 'Writing R documentation files' in the 'Writing R
Extensions' manual.
Packages suggested but not available for checking: 'pmg' 'SVGAnnotation'
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    R      3.6Mb
    help  10.6Mb
    libs   5.1Mb
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.5/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.5/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:297:17: warning: 'json_shared_string::len' will be initialized after [-Wreorder]
  libjson/Source/JSONSharedString.h:295:40: warning:   'json_shared_string::json_shared_string_internal* json_shared_string::_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:180:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONSharedString.h:182:9: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:79:7: warning: 'JSONStream::state' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:76:28: warning:   'void (* JSONStream::call)(void*, void*)' [-Wreorder]
  JSONStream.cpp:8:1: warning:   when initialized here [-Wreorder]
  libjson/Source/JSONStream.h:77:27: warning: 'JSONStream::err_call' will be initialized after [-Wreorder]
  libjson/Source/JSONStream.h:75:17: warning:   'json_string JSONStream::buffer' [-Wreorder]
  JSONStream.cpp:12:1: warning:   when initialized here [-Wreorder]
  libjson/Source/internalJSONNode.h:257:18: warning: 'internalJSONNode::_name_encoded' will be initialized after [-Wreorder]
  libjson/Source/internalJSONNode.h:256:17: warning:   'json_string internalJSONNode::_name' [-Wreorder]
  internalJSONNode.cpp:78:1: warning:   when initialized here [-Wreorder]
See 'd:/Rcompile/CRANpkg/local/3.5/RJSONIO.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rmosek.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/robets.Rcheck/00install.out' for details.
Package required but not available: 'Rcplex'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ROracle.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/RSAlgaeR.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Rsampletrees.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/3.5/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.5/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Depends: includes the non-default packages:
  'biwt' 'cairoDevice' 'fBasics' 'gplots' 'gWidgets' 'gWidgetsRGtk2'
  'minerva' 'parmigene' 'stringr' 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

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

Matrix products: default

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

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

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

loaded via a namespace (and not attached):
[1] compiler_3.5.0
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: Shapes and Points, Tooltips are Title + 1 Line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    libs      8.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ryouready.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/scorecardModelUtils.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ScottKnottESD.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    2.4Mb
    libs   3.5Mb
Running examples in 'secrlinear-Ex.R' failed
The error most likely occurred in:

> ### Name: Arvicola
> ### Title: Water Vole Capture Dataset
> ### Aliases: arvicola
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> head(traps(arvicola))
          x      y
0.A  164.86 609.69
0.B  164.86 609.69
20.A 163.85 629.66
20.B 163.85 629.66
40.A 164.88 649.19
40.B 164.88 649.19
> 
> ## for speed, pre-compute distance matrix
> userd <- networkdistance (traps(arvicola), glymemask, glymemask)
> ## fit model
> glymefit <- secr.fit(arvicola, mask = glymemask, trace = FALSE,
+                      details = list(userdist = userd))
Warning in check3D(object) :
  secr 3.0 requires 3-D capthist; using updateCH() to convert
Warning in autoini(ch, msk, binomN = details$binomN, ignoreusage = details$ignoreusage) :
  'autoini' failed to find g0; setting initial g0 = 0.1
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/semPlot.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/SensoMineR.Rcheck/00install.out' for details.
Depends: includes the non-default packages:
  'hdrcde' 'coda' 'MASS' 'bayesm' 'mnormt' 'spatstat'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/soil.spec.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/spduration.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'rcytoscapejs'
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.5/spectrolab.Rcheck/00install.out' for details.
Running examples in 'spm12r-Ex.R' failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> res = install_spm12(install_dir = tdir)
cloning into 'D:\temp\RtmpwVbi2G\file31e9c1f64127/spm12'...
Error in git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",  : 
  Error in 'git2r_clone': unknown certificate check failure
Calls: install_spm12 -> <Anonymous>
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
Running examples in 'steemr-Ex.R' failed
The error most likely occurred in:

> ### Name: follower_df
> ### Title: A id list of an id's followers from steemdb.com
> ### Aliases: follower_df
> 
> ### ** Examples
> 
> follower_df()
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to steemdb.com port 443: Connection refused
Calls: follower_df -> <Anonymous> -> curlPerform -> <Anonymous> -> fun
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/StMoMo.Rcheck/00install.out' for details.
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("stringdist")
  Loading required package: stringdist
  Warning: stack imbalance in 'vapply', 46 then 45
  Warning: stack imbalance in '{', 39 then 38
  -- 1. Failure: elementary seq_sim test (@testStringsim.R#62)  ------------------
  seq_sim(list(1:3, 2:4), list(1:3)) not equal to stringsim(c("abc", "bcd"), "abc").
  1/2 mismatches
  [1] 0.333 - 1 == -0.667
  
  == testthat results  ===========================================================
  OK: 416 SKIPPED: 1 FAILED: 1
  1. Failure: elementary seq_sim test (@testStringsim.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/stUPscales.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  1: expect_true(process_exists(child_id)) at testthat/test-termination.R:34
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: process_exists(child_id)
  5: isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  OK: 58 SKIPPED: 3 FAILED: 2
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(subprocess)
  > 
  > # See for more details:
  > # https://github.com/hadley/testthat/issues/144
  > # https://github.com/hadley/testthat/issues/86
  > # https://github.com/luckyrandom/cmaker/commit/b85813ac2b7aef69932eca8fbb4fa0ec225e0af0
  > #
  > # When R CMD check runs tests, it sets R_TESTS. When the tests
  > # themeselves run R CMD xxxx, as is the case with the tests in
  > # devtools, having R_TESTS set causes errors because it confuses
  > # the R subprocesses. Unsetting it here avoids those problems.
  > #
  > # We need this because we spawn child R processes and they get very
  > # confused if this variable (R_TESTS) is present in their environment.
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("subprocess")
  Keine Instanzen verfgbar.
  -- 1. Failure: child process is terminated in Windows (@test-termination.R#33)  
  `child_id` has length 0, not length 1.
  
  -- 2. Error: child process is terminated in Windows (@test-termination.R#34)  --
  `pid` must be a single integer value
  1: expect_true(process_exists(child_id)) at testthat/test-termination.R:34
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: process_exists(child_id)
  5: isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  OK: 58 SKIPPED: 3 FAILED: 2
  1. Failure: child process is terminated in Windows (@test-termination.R#33) 
  2. Error: child process is terminated in Windows (@test-termination.R#34) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Packages suggested but not available for checking: 'sylly.de' 'sylly.es'
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Packages suggested but not available for checking:
  'Rcampdf' 'Rpoppler' 'tm.lexicon.GeneralInquirer'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TPMplt.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TriMatch.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/tsBSS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TSCS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TSF.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/tsoutliers.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/TSPred.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/tsSelect.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'gdalUtils::gdal_rasterize' by 'sf::gdal_rasterize' when loading 'uavRmp'
See 'd:/Rcompile/CRANpkg/local/3.5/uavRmp.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/updog.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'vaers' 'vaersND'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/VDAP.Rcheck/00install.out' for details.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.2Mb
    help   2.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/VIMGUI.Rcheck/00install.out' for details.
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/WaveletArima.Rcheck/00install.out' for details.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    exampleData   1.4Mb
    examples      4.5Mb
    libs          4.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/Xplortext.Rcheck/00install.out' for details.
Running 'test-all.R' [38s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > test_check("zoon")
  Loading required package: zoon
  Loading required package: raster
  Loading required package: sp
  -- 1. Failure: Expected errors (@testTransformCRS.R#39)  -----------------------
  `workflow(...)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 237 SKIPPED: 30 FAILED: 1
  1. Failure: Expected errors (@testTransformCRS.R#39) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ZRA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.2Mb
    libs                    6.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error in re-building vignettes:
  ...


Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1788e2bb68d48.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1788e2bb68d48.png': No such file or directory
Quitting from lines 91-93 (ActisoftR.Rmd) 
Error: processing vignette 'ActisoftR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Namespaces in Imports field not imported from:
  ‘plotly’ ‘shinydashboard’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Error: processing vignette 'additivityTests-vignette.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/adiv.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘HiTC’
Package unavailable to check Rd xrefs: ‘HiTC’
Found the following significant warnings:
  ADM3.c:34:19: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:31: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:34:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:61: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:73: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:39:57: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:52:6: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:54:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:55:42: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:10: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ADM3.c:56:38: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ADM3.Rcheck/00install.out’ for details.
ADM3: no visible global function definition for ‘read.table’
ADM3: no visible global function definition for ‘write.table’
dLRs: no visible global function definition for ‘IQR’
dLRs: no visible global function definition for ‘na.omit’
dLRs: no visible global function definition for ‘qnorm’
plotADM3: no visible global function definition for ‘plot’
plotADM3: no visible global function definition for ‘abline’
plotADM3: no visible global function definition for ‘segments’
Undefined global functions or variables:
  IQR abline na.omit plot qnorm read.table segments write.table
Consider adding
  importFrom("graphics", "abline", "plot", "segments")
  importFrom("stats", "IQR", "na.omit", "qnorm")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AFM.Rcheck/00install.out’ for details.
IIR: no visible global function definition for ‘qnorm’
TIR: no visible global function definition for ‘qnorm’
agreement: no visible global function definition for ‘var’
agreement: no visible global function definition for ‘pchisq’
agreement: no visible global function definition for ‘dnorm’
agreement: no visible global function definition for ‘qnorm’
html.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘plot’
plot.report: no visible global function definition for ‘axis’
plot.report: no visible global function definition for ‘points’
unified.agreement: no visible global function definition for ‘lm’
unified.agreement: no visible global function definition for ‘qnorm’
unified.agreement: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  axis dnorm lm pchisq plot pnorm points qnorm var
Consider adding
  importFrom("graphics", "axis", "plot", "points")
  importFrom("stats", "dnorm", "lm", "pchisq", "pnorm", "qnorm", "var")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-67 (ahn.Rmd) 
Error: processing vignette 'ahn.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/AIG.Rcheck/00install.out’ for details.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  matrix.c:629:8: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:631:49: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  matrix.c:632:39: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/amei.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Loading required package: network
network: Classes for Relational Data
Version 1.13.0.1 created on 2015-08-31.
copyright (c) 2005, Carter T. Butts, University of California-Irvine
                    Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Martina Morris, University of Washington
                    Skye Bender-deMoll, University of Washington
 For citation information, type citation("network").
 Type help("network-package") to get started.


Execution halted
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/anapuce.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
  WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ANLP.Rcheck/00install.out’ for details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by weka.core.WekaPackageClassLoaderManager (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/RWekajars/java/weka.jar) to method java.lang.ClassLoader.defineClass(java.lang.String,byte[],int,int,java.security.ProtectionDomain)
WARNING: Please consider reporting this to the maintainers of weka.core.WekaPackageClassLoaderManager
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-73 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Error in loadNamespace(name) : there is no package called 'devtools'
trying URL 'https://cloud.r-project.org/bin/macosx/el-capitan/contrib/3.5/apercu_0.2.3.tgz'
Content type 'application/x-gzip' length 27068 bytes (26 KB)
==================================================
downloaded 26 KB

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

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

Error in loadNamespace(name) : there is no package called 'BiocInstaller'
Error in loadNamespace(name) : there is no package called 'devtools'
Error: processing vignette 'help.Rmd' failed with diagnostics:
there is no package called ‘markdown’
Execution halted
Running examples in ‘apaStyle-Ex.R’ failed
The error most likely occurred in:

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

Returned 'NA'!


No TSN found for species 'Juniperus occidentalis'!


Retrieving data for taxon 'Pinus strobus'





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

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


Returned 'NA'!


No TSN found for species 'Pinus strobus'!


Execution halted
Packages suggested but not available for checking:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’
Found the following significant warnings:
  am.c:275:9: warning: comparison of array 'readByte' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/aqr.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘TDA’
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'argparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R             2.2Mb
    help          1.1Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘GLAD’
Packages suggested but not available for checking:
  ‘GLAD’ ‘sfit’ ‘expectile’ ‘HaarSeg’ ‘mpcbs’
Package unavailable to check Rd xrefs: ‘GLAD’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Arothron.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: ‘cacheSweave’ ‘weaver’
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  au.c:375:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int)') with an expression of type 'au_instance_t *(SEXP, float, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int)') [-Wincompatible-pointer-types]
  au.c:376:2: warning: incompatible pointer types initializing 'struct audio_instance *(*)(SEXP, float, int, int)' (aka 'struct audio_instance *(*)(struct SEXPREC *, float, int, int)') with an expression of type 'au_instance_t *(SEXP, float, int, int)' (aka 'struct au_instance *(struct SEXPREC *, float, int, int)') [-Wincompatible-pointer-types]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/audio.Rcheck/00install.out’ for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.7Mb
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    libs  20.8Mb
best: no visible global function definition for ‘optim’
randomboards: no visible global function definition for ‘runif’
randomprobs: no visible global function definition for ‘runif’
Undefined global functions or variables:
  optim runif
Consider adding
  importFrom("stats", "optim", "runif")
to your NAMESPACE file.
File ‘aylmer/libs/aylmer.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘aylmer.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘aylmer.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   2.4Mb
Package suggested but not available for checking: ‘philr’
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: philr::phylo2sbp at testthat/test-sbp.R:5
  2: getExportedValue(pkg, name)
  3: asNamespace(ns)
  4: getNamespace(ns)
  5: tryCatch(loadNamespace(name), error = function(e) stop(e))
  6: tryCatchList(expr, classes, parentenv, handlers)
  7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  8: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-sbp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BALCONY.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANFF.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BANOVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ArrayExpress’
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 46-49 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...

Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BatchGetSymbols.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘doMPI’
Package unavailable to check Rd xrefs: ‘Rmpi’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BAT.Rcheck/00install.out’ for details.
Package required but not available: ‘mritc’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bayesCL.Rcheck/00install.out’ for details.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 47.6Mb
  sub-directories of 1Mb or more:
    libs  46.9Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "Error in sampler$call_sampler(args_list[[i]]) : "
  [2] "  c++ exception (unknown reason)"                
  Stan model 'dfa' does not contain samples.
  Stan model 'dfa' does not contain samples.
  ── 1. Error: (unknown) (@test-fit.R#8)  ────────────────────────────────────────
  attempt to set an attribute on NULL
  1: fit_dfa(y = y, num_trends = 1, iter = 800, chains = 1) at testthat/test-fit.R:8
  2: rstan::monitor(e)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-fit.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  11.7Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
installed size is 61.2Mb
  sub-directories of 1Mb or more:
    libs  60.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.5Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs  15.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Depends: includes the non-default packages:
  ‘lme4’ ‘MASS’ ‘VGAM’ ‘mvtnorm’ ‘matrixcalc’ ‘coda’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Bayesthresh.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘MASS’ ‘VGAM’ ‘coda’ ‘lme4’ ‘matrixcalc’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Found the following significant warnings:

  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.5Mb
File ‘BayHap/libs/BayHap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘mcmc.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘mcmc.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.2Mb
Packages suggested but not available for checking:
  ‘beadarrayExampleData’ ‘lumi’
Running examples in ‘beadarrayFilter-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 59.2Mb
  sub-directories of 1Mb or more:
    libs  57.8Mb
'library' or 'require' call to ‘multcomp’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 26.3Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
binommh.default : log_lik: no visible global function definition for
  ‘dbinom’
binommh.default: no visible global function definition for ‘dbinom’
binommh.default: no visible global function definition for ‘runif’
binommh.formula: no visible global function definition for
  ‘model.frame’
binommh.formula: no visible global function definition for
  ‘model.matrix’
binommh.formula: no visible global function definition for
  ‘model.response’
expmh.default : log_lik: no visible global function definition for
  ‘dexp’
expmh.default: no visible global function definition for ‘dexp’
expmh.default: no visible global function definition for ‘runif’
expmh.formula: no visible global function definition for ‘model.frame’
expmh.formula: no visible global function definition for ‘model.matrix’
expmh.formula: no visible global function definition for
  ‘model.response’
poissmh.default : log_lik: no visible global function definition for
  ‘dpois’
poissmh.default: no visible global function definition for ‘dpois’
poissmh.default: no visible global function definition for ‘runif’
poissmh.formula: no visible global function definition for
  ‘model.frame’
poissmh.formula: no visible global function definition for
  ‘model.matrix’
poissmh.formula: no visible global function definition for
  ‘model.response’
Undefined global functions or variables:
  dbinom dexp dpois model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "dbinom", "dexp", "dpois", "model.frame",
             "model.matrix", "model.response", "runif")
to your NAMESPACE file.
Package required but not available: ‘TargetScore’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 141.1Mb
  sub-directories of 1Mb or more:
    include  141.0Mb
Running ‘testthat.R’ [2s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library("testthat")
  > library("bib2df")
  > test_check("bib2df")
  ── 1. Failure: bib2df() throws error messages (@tests.R#70)  ───────────────────
  `bib2df("https://www.example.com/data/x.bib")` threw an error with unexpected message.
  Expected match: "Invalid URL: File is not readable."
  Actual message: "Timeout was reached: Connection timed out after 10009 milliseconds"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 19 SKIPPED: 0 FAILED: 1
  1. Failure: bib2df() throws error messages (@tests.R#70) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.8Mb
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BIGL.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Transformation introduced infinite values in continuous x-axis
Warning: Transformation introduced infinite values in continuous y-axis
Warning: Removed 199 rows containing non-finite values (stat_contour).
Warning in normalizePath(f2) :
  path[1]="./webshot101686b25b69.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot101686b25b69.png': No such file or directory
Quitting from lines 244-247 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bigpca.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
bigRR: no visible global function definition for ‘gaussian’
bigRR.default: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘gaussian’
bigRR.formula: no visible global function definition for ‘as.formula’
bigRR.formula: no visible global function definition for ‘model.frame’
bigRR.formula: no visible global function definition for ‘model.matrix’
bigRR.formula: no visible global function definition for
  ‘model.response’
bigRR_update: no visible global function definition for ‘gaussian’
hugeRR: no visible global function definition for ‘gaussian’
hugeRR_update: no visible global function definition for ‘gaussian’
plot.bigRR: no visible global function definition for ‘par’
plot.bigRR: no visible global function definition for ‘plot’
plot.bigRR: no visible global function definition for ‘rgb’
Undefined global functions or variables:
  as.formula gaussian model.frame model.matrix model.response par plot
  rgb
Consider adding
  importFrom("grDevices", "rgb")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "as.formula", "gaussian", "model.frame",
             "model.matrix", "model.response")
to your NAMESPACE file.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      6.0Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 37-44 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’ ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   2.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bioacoustics.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 64-67 (BioCircos.Rmd) 
Error: processing vignette 'BioCircos.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘BiocVersion’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Biocomb.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocStyle’
Running ‘test-all.R’ [9s/13s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  ── 5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17)  
  `gbLocation("123^125")` threw an error with unexpected message.
  Expected match: "Inadmissible range"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 267 SKIPPED: 1 FAILED: 5
  1. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#6) 
  2. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#9) 
  3. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#13) 
  4. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#14) 
  5. Failure: Location descriptors parse correctly (@test-01-gbLocation.r#17) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (IntroBiofiles.Rnw) 
Error: processing vignette 'IntroBiofiles.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.0Mb
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 48-51 (BioInstaller.Rmd) 
Error: processing vignette 'BioInstaller.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/BioPhysConnectoR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
extractPDB : atom.select : sel.txt2nums: no visible global function
  definition for ‘na.omit’
extractPDB : read.pdb: no visible global function definition for
  ‘na.omit’
mat.read: no visible global function definition for ‘read.table’
mat.write: no visible global function definition for ‘write.table’
scpcp: no visible global function definition for ‘pgamma’
sim : sim.func: no visible global function definition for ‘write.table’
simc: no visible global function definition for ‘write.table’
simc : simc.func: no visible global function definition for
  ‘write.table’
sims: no visible global function definition for ‘write.table’
sims : sims.func: no visible global function definition for
  ‘write.table’
Undefined global functions or variables:
  na.omit pgamma read.table write.table
Consider adding
  importFrom("stats", "na.omit", "pgamma")
  importFrom("utils", "read.table", "write.table")
to your NAMESPACE file.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
plot.BIPOD: no visible global function definition for ‘par’
plot.BIPOD: no visible global function definition for ‘matplot’
plot.BIPOD: no visible global function definition for ‘abline’
plot.BIPOD: no visible global function definition for ‘plot’
plot.BIPOD: no visible global function definition for ‘density’
plot.BIPOD: no visible global function definition for ‘curve’
plot.BIPOD: no visible global function definition for ‘dlnorm’
plot.BIPOD: no visible global function definition for ‘dnorm’
plot.BIPOD: no visible global function definition for ‘acf’
plot.BIPOD: no visible global function definition for ‘pairs’
plot.BIPOD : standfun: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘sd’
plot.BIPOD: no visible global function definition for ‘points’
plot.BIPOD: no visible global function definition for ‘tail’
plot.BIPOD: no visible global function definition for ‘matlines’
plot.BIPOD: no visible binding for global variable ‘quantile’
plot.BIPOD: no visible global function definition for ‘lines’
Undefined global functions or variables:
  abline acf curve density dlnorm dnorm lines matlines matplot pairs
  par plot points quantile sd tail
Consider adding
  importFrom("graphics", "abline", "curve", "lines", "matlines",
             "matplot", "pairs", "par", "plot", "points")
  importFrom("stats", "acf", "density", "dlnorm", "dnorm", "quantile",
             "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’ ‘cairoDevice’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
blighty: no visible global function definition for ‘par’
blighty: no visible global function definition for ‘polygon’
blighty: no visible global function definition for ‘points’
blighty: no visible global function definition for ‘box’
blighty: no visible global function definition for ‘axis’
blighty: no visible global function definition for ‘abline’
map.scale: no visible global function definition for ‘locator’
map.scale: no visible global function definition for ‘segments’
map.scale: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘locator’
north.pointer: no visible global function definition for ‘text’
north.pointer: no visible global function definition for ‘arrows’
north.pointer: no visible global function definition for ‘segments’
sqlimits: no visible global function definition for ‘frame’
sqlimits: no visible global function definition for ‘par’
Undefined global functions or variables:
  abline arrows axis box frame locator par points polygon segments text
Consider adding
  importFrom("graphics", "abline", "arrows", "axis", "box", "frame",
             "locator", "par", "points", "polygon", "segments", "text")
to your NAMESPACE file.
installed size is 38.1Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
Running examples in ‘blockingChallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: makeblocks
> ### Title: Creates strata of size 'bsize' aiming to minimize within strata
> ###   distance.
> ### Aliases: makeblocks
> ### Keywords: Challenge Stratification algorithm
> 
> ### ** Examples
> 
> ## IN THESE EXAMPLES YOU NEED TO LOAD THE R PACKAGE 
> #  'optmatch'.  OTHERWISE, THEY WILL RUN IN A CODE CHECK MODE.
> # library(optmatch)
> ###### 		Usage 1		##########
> data(nh0506)
> ## Don't show: 
> 	nh0506 <- nh0506[1:13,]
> ## End(Don't show)
> res <- makeblocks(nh0506, bsize=4, maxItr=15, 
+          vars=c("female","age","black","hispanic","education","povertyr"))
Iteration no. 1 :: Error in pairmatch(distmat.temp1, controls = bsize - 1) : 
  could not find function "pairmatch"
Calls: makeblocks -> eval -> eval
Execution halted
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  12.2Mb
installed size is 35.5Mb
  sub-directories of 1Mb or more:
    libs  35.2Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/boclust.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘sangerseqR’
print.boolprob: no visible global function definition for ‘plot’
print.boolprof: no visible global function definition for ‘plot’
start_msg: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription plot
Consider adding
  importFrom("graphics", "plot")
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
installed size is 328.9Mb
  sub-directories of 1Mb or more:
    include    3.0Mb
    lib      325.6Mb
installed size is 69.7Mb
  sub-directories of 1Mb or more:
    libs  69.3Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bootnet.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/bpca.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘RGtk2’ ‘cairoDevice’
File ‘brainwaver/libs/brainwaver.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘connexity_small_world.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 34.0Mb
  sub-directories of 1Mb or more:
    libs  33.9Mb
Running examples in ‘breathteststan-Ex.R’ failed
The error most likely occurred in:

> ### Name: stan_fit
> ### Title: Bayesian Stan fit to 13C Breath Data
> ### Aliases: stan_fit
> 
> ### ** Examples
> 
> library(breathtestcore)
> suppressPackageStartupMessages(library(dplyr))
> d = breathtestcore::simulate_breathtest_data(n_records = 3) # default 3 records
> data = breathtestcore::cleanup_data(d$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 120, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = "m")$m), beta = as.vector(rstan::extract(fit, permuted = TRUE, 
         pars = "beta")$beta), k = as.vector(rstan::extract(fit, permuted = TRUE, pars = "k")$k))
  3: stop(gettextf("arguments imply differing number of rows: %s", paste(unique(nrows), 
         collapse = ", ")), domain = NA)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 7 FAILED: 2
  1. Error: Result with default parameters is tbl_df with required columns (@test_coef_by_group.R#16) 
  2. Error: Data that cannot be fitted with nls_list/nlme work with stan_fit (@test_stan_fit_2.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘pasilla’
Packages required but not available: ‘DiffBind’ ‘Rsamtools’

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

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

    intersect, setdiff, setequal, union


Attaching package: 'c3'

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

    %>%

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

    grid, legend

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb3c71d491160.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb3c71d491160.png': No such file or directory
Quitting from lines 56-65 (examples.Rmd) 
Error: processing vignette 'examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cairoDevice.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
rgdal: version: 1.2-18, (SVN revision 718)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.1.3, released 2017/20/01
 Path to GDAL shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/gdal
 GDAL binary built with GEOS: FALSE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/rgdal/proj
 Linking to sp version: 1.2-7 
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-54 (DataExtraction.Rmd) 
Error: processing vignette 'DataExtraction.Rmd' failed with diagnostics:
cannot find ExifTool
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.6Mb
Running examples in ‘caRpools-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   3.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
     validation strategies for spatial-temporal models. To decrease
     overfitting and improve model performances, the package implements
     a forward feature selection that selects suitable predictor
     variables in view to their contribution to the target-oriented
     performance.

_D_e_t_a_i_l_s:

     'caret' Applications for Spatio-Temporal models

_A_u_t_h_o_r(_s):

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


PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotb12b414ebbf6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotb12b414ebbf6.png': No such file or directory
Quitting from lines 65-73 (CAST-intro.Rmd) 
Error: processing vignette 'CAST-intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
Found the following significant warnings:
  ./MCMC_prob.h:2091:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CCMnet.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   2.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
plot.CellularAutomaton: no visible global function definition for
  ‘image’
Undefined global functions or variables:
  image
Consider adding
  importFrom("graphics", "image")
to your NAMESPACE file.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.5Mb
Running examples in ‘census-Ex.R’ failed
The error most likely occurred in:

> ### Name: getCensus
> ### Title: Scrape US Census Data
> ### Aliases: getCensus
> 
> ### ** Examples
> 
> radius <- 5
> cities <- c("Boston", "Los Angeles")
> df <- getCensus(cities, radius)
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Boston&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Boston"
Information from URL : http://maps.googleapis.com/maps/api/geocode/json?address=Los%20Angeles&sensor=false
Warning: geocode failed with status OVER_QUERY_LIMIT, location = "Los Angeles"
Error in `[.data.frame`(geo.reply, , c("locality", "lon", "lat")) : 
  undefined columns selected
Calls: getCensus -> [ -> [.data.frame
Execution halted
Found the following hidden files and directories:
  .project
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
get.switch.time: warning in uniroot(f = switch.func, int =
  c(last_boundary, boundary), lower = last_boundary, upper = boundary,
  maxiter = 1000, tol = tol, e): partial argument match of 'int' to
  'interval'
plot.cggd: warning in axis(4, at = b[nrow(b), ], label = paste(cnums),
  cex = 0.8, adj = 0): partial argument match of 'label' to 'labels'
plot.cggd: no visible global function definition for ‘gen.beta’
plotCVcggd: no visible binding for global variable ‘cv’
plotCVcggd: no visible binding for global variable ‘cv.error’
predict.cggd: no visible binding for global variable ‘max.tk’
predict.cggd: no visible global function definition for ‘gen.beta’
Undefined global functions or variables:
  cv cv.error gen.beta max.tk
S3 methods shown with full name in documentation object 'plot.cggd':
  ‘plot.cggd’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
CGH.fused.lasso.one.fast: no visible global function definition for
  ‘lowess’
L2L1ExpandFit: no visible global function definition for
  ‘L2L1PathExtract’
consensusFDR: no visible global function definition for ‘pbinom’
my.mad: no visible global function definition for ‘median’
output.cghFLasso: no visible global function definition for
  ‘write.table’
plot.CGH.FL.All: no visible global function definition for ‘plot’
plot.CGH.FL.All: no visible global function definition for ‘segments’
plot.CGH.FL.All: no visible global function definition for ‘text’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘rainbow’
plot.CGH.FL.Consensus: no visible global function definition for ‘plot’
plot.CGH.FL.Consensus: no visible global function definition for
  ‘segments’
plot.CGH.FL.Consensus: no visible global function definition for ‘gray’
plot.CGH.FL.Consensus: no visible global function definition for ‘text’
plot.CGH.FL.Single: no visible global function definition for ‘plot’
plot.CGH.FL.Single: no visible global function definition for ‘gray’
plot.CGH.FL.Single: no visible global function definition for
  ‘segments’
plot.CGH.FL.Single: no visible global function definition for ‘text’
plot.cghFLasso: no visible global function definition for ‘plot’
plot.cghFLasso: no visible global function definition for ‘gray’
plot.cghFLasso: no visible global function definition for ‘abline’
plot.cghFLasso: no visible global function definition for ‘points’
segment.score: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  L2L1PathExtract abline gray lowess median pbinom plot pnorm points
  rainbow segments text write.table
Consider adding
  importFrom("grDevices", "gray", "rainbow")
  importFrom("graphics", "abline", "plot", "points", "segments", "text")
  importFrom("stats", "lowess", "median", "pbinom", "pnorm")
  importFrom("utils", "write.table")
to your NAMESPACE file.
S3 methods shown with full name in documentation object 'plot.cghFLasso':
  ‘plot.cghFLasso’

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  costfunctions.c:33:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  costfunctions.c:57:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/changepoint.np.Rcheck/00install.out’ for details.
Running ‘test_changepoints.R’ [1s/1s]
Running the tests in ‘tests/test_changepoints.R’ failed.
Last 13 lines of output:
  [1] 88 10
  [1] 12 10
  [1] 89 10
  [1] 11 10
  [1] 90 10
  [1] 10 10
  [1] 77 10
  [1] 23 10
  > stopifnot(changepoints_mod@changepoints == 77)
  > 
  > # test rank one
  > res_ro = rank_one(scp_data, init, update_w=0.1, regularizer=0.1)
  > stopifnot(res_ro$tau == 56)
  Error: res_ro$tau == 56 is not TRUE
  Execution halted
Package suggested but not available for checking: ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CHAT.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 160-170 (checkmate.Rmd) 
Error: processing vignette 'checkmate.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in library.dynam(lib, package, package.lib):
 shared object 'plyr.so' not found
Execution halted
Packages suggested but not available for checking:
  ‘GenomicInteractions’ ‘Gviz’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-105 (Visualising_Interactions.Rmd) 
Error: processing vignette 'Visualising_Interactions.Rmd' failed with diagnostics:
there is no package called 'GenomicInteractions'
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 42-44 (access_childes_db.Rmd) 
Error: processing vignette 'access_childes_db.Rmd' failed with diagnostics:
SSL certificate problem: Invalid certificate chain
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CircE.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
CircE.Plot: no visible global function definition for ‘dev.new’
CircE.Plot: no visible global function definition for ‘par’
CircE.Plot: no visible global function definition for ‘plot’
CircE.Plot: no visible global function definition for ‘axis’
CircE.Plot: no visible global function definition for ‘title’
CircE.Plot: no visible global function definition for ‘text’
CircE.Plot: no visible global function definition for ‘points’
CircE.Plot: no visible global function definition for ‘abline’
CircE.Plot: no visible global function definition for ‘segments’
Undefined global functions or variables:
  abline axis dev.new par plot points segments text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "abline", "axis", "par", "plot", "points",
             "segments", "text", "title")
to your NAMESPACE file.
Package required but not available: ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘FRAPO’
Package unavailable to check Rd xrefs: ‘FRAPO’
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.2Mb
cv.clogitL1 : <anonymous>: no visible global function definition for
  ‘var’
plot.clogitL1: no visible global function definition for ‘matplot’
plot.clogitL1: no visible global function definition for ‘legend’
plot.clogitL1: no visible global function definition for ‘text’
plot.cv.clogitL1: no visible global function definition for ‘matplot’
plot.cv.clogitL1: no visible global function definition for ‘matlines’
plot.cv.clogitL1: no visible global function definition for ‘points’
plot.cv.clogitL1: no visible global function definition for ‘axis’
plot.cv.clogitL1: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis legend matlines matplot points text var
Consider adding
  importFrom("graphics", "abline", "axis", "legend", "matlines",
             "matplot", "points", "text")
  importFrom("stats", "var")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/clpAPI.Rcheck/00install.out’ for details.
Packages required but not available: ‘rggobi’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Package suggested but not available for checking: ‘SingleCellExperiment’
Package suggested but not available for checking: ‘moe430a.db’
Error in re-building vignettes:
  ...

    expand.grid

Loading required package: XML

Attaching package: ‘XML’

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

    toHTML

Loading required package: GO.db

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/colourvision.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Combine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages suggested but not available for checking:
  ‘inSilicoDb’ ‘mogene10sttranscriptcluster.db’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompetingRisk.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Utility.c:162:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:187:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:211:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:392:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:417:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  Utility.c:442:8: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/CompRandFld.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 47.4Mb
  sub-directories of 1Mb or more:
    libs  46.3Mb
Found the following significant warnings:
  date.cpp:167:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:167:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:169:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:171:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:27: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:34: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
  date.cpp:173:41: warning: ISO C++11 does not allow conversion from string literal to 'char *' [-Wwritable-strings]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ConvCalendar.Rcheck/00install.out’ for details.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   6.5Mb
Package suggested but not available for checking: ‘ProData’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
CosmoPhotoZestimator: no visible global function definition for
  ‘predict’
computeCombPCA: no visible global function definition for ‘prcomp’
computeDiagPhotoZ: no visible global function definition for ‘sd’
computeDiagPhotoZ: no visible global function definition for ‘median’
computeDiagPhotoZ: no visible global function definition for ‘mad’
glmPredictPhotoZ: no visible global function definition for ‘predict’
glmTrainPhotoZ: no visible global function definition for ‘glm’
glmTrainPhotoZ: no visible global function definition for ‘Gamma’
glmTrainPhotoZ: no visible global function definition for
  ‘inverse.gaussian’
plotDiagPhotoZ: no visible global function definition for ‘median’
plotDiagPhotoZ: no visible global function definition for ‘mad’
Undefined global functions or variables:
  Gamma glm inverse.gaussian mad median prcomp predict sd
Consider adding
  importFrom("stats", "Gamma", "glm", "inverse.gaussian", "mad",
             "median", "prcomp", "predict", "sd")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.3Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Error in re-building vignettes:
  ...

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

    legend

Loading required package: rugarch
Loading required package: parallel

Attaching package: 'rugarch'

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

    sigma


Attaching package: 'rmgarch'

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

    first, last

Quitting from lines 217-225 (CovarianceEstimation.Rmd) 
Error: processing vignette 'CovarianceEstimation.Rmd' failed with diagnostics:
all(sapply(args, function(x) is.zoo(x) || !is.plain(x) || (is.plain(x) &&  .... is not TRUE
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  37.5Mb
find.antimodeMLE: no visible global function definition for ‘par’
find.decreasingMLE: no visible global function definition for ‘chull’
find.decreasingMLE: no visible global function definition for ‘points’
find.increasingMLE: no visible global function definition for ‘chull’
find.increasingMLE: no visible global function definition for ‘points’
find.modeMLE: no visible global function definition for ‘par’
plot.CPHshape: no visible global function definition for ‘plot’
plot.CPHshape: no visible global function definition for ‘segments’
plot.CPHshape: no visible global function definition for ‘abline’
plot.CPHshape: no visible global function definition for ‘grey’
plot.CPHshape: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline chull grey par plot points segments
Consider adding
  importFrom("grDevices", "chull", "grey")
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cplexAPI.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 77-78 (cranly.Rmd) 
Error: processing vignette 'cranly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘clusterProfiler’
Error in re-building vignettes:
  ...
    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: IRanges
Loading required package: S4Vectors

Attaching package: 'S4Vectors'

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

    expand.grid


Attaching package: 'IRanges'

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

    trim


Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'clusterProfiler'
Execution halted
Package suggested but not available for checking: ‘Rglpk’
Error in re-building vignettes:
  ...
  Used default patient IDs!
Loading required package: dplyr

Attaching package: ‘dplyr’

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

Timing stopped at: 149.6 1.468 254.9
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/crplyr.Rcheck/00install.out’ for details.
installed size is 21.9Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
D.SN: no visible global function definition for ‘dnorm’
D.SN: no visible global function definition for ‘pnorm’
beta2cp: no visible global function definition for ‘pnorm’
cSFM.est: no visible global function definition for ‘optim’
cSFM.est: no visible global function definition for ‘qnorm’
cSFM.est: no visible global function definition for ‘cor’
case2.b.initial: no visible global function definition for ‘var’
case2.gr: no visible global function definition for ‘pnorm’
case2.gr: no visible global function definition for ‘dnorm’
case2.unmll.optim: no visible global function definition for ‘pnorm’
cp2beta: no visible global function definition for ‘qnorm’
data.generator.y.F: no visible global function definition for ‘cov2cor’
data.generator.y.F: no visible global function definition for ‘rnorm’
data.generator.y.F : <anonymous>: no visible global function definition
  for ‘pnorm’
g: no visible global function definition for ‘dnorm’
g: no visible global function definition for ‘pnorm’
predict.cSFM : <anonymous>: no visible global function definition for
  ‘qnorm’
predict.cSFM: no visible global function definition for ‘qnorm’
predict.cSFM: no visible global function definition for ‘pnorm’
Undefined global functions or variables:
  cor cov2cor dnorm optim pnorm qnorm rnorm var
Consider adding
  importFrom("stats", "cor", "cov2cor", "dnorm", "optim", "pnorm",
             "qnorm", "rnorm", "var")
to your NAMESPACE file.
installed size is 76.4Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
    doc    4.1Mb
    libs  66.1Mb
Package which this enhances but not available for checking: ‘pbdMPI’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/cudaBayesreg.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘MCMCpack’ ‘mvtnorm’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
cudiaDet: no visible global function definition for ‘model.frame’
cudiaDet: no visible global function definition for ‘model.response’
cudiaDet: no visible binding for global variable ‘sd’
cudiaDet: no visible global function definition for ‘rdirichlet’
cudiaDet: no visible global function definition for ‘rnorm’
cudiaDet: no visible global function definition for ‘lm.ridge’
plot.cudia: no visible global function definition for ‘par’
plot.cudia: no visible global function definition for ‘plot’
Undefined global functions or variables:
  lm.ridge model.frame model.response par plot rdirichlet rnorm sd
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "model.frame", "model.response", "rnorm", "sd")
to your NAMESPACE file.
Running examples in ‘curl-Ex.R’ failed
The error most likely occurred in:

> ### Name: curl_echo
> ### Title: Echo Service
> ### Aliases: curl_echo
> 
> ### ** Examples
> 
> h <- handle_setform(new_handle(), foo = "blabla", bar = charToRaw("test"),
+ myfile = form_file(system.file("DESCRIPTION"), "text/description"))
> formdata <- curl_echo(h)
Error in curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle) : 
  Callback aborted
Calls: curl_echo -> curl_fetch_memory
Execution halted
Running ‘spelling.R’ [1s/2s]
  Comparing ‘spelling.Rout’ to ‘spelling.Rout.save’ ... OK
  Running ‘testthat.R’ [7s/50s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("curl")
  This is libcurl version 7.43.0 with SecureTransport 
  Using test server: http://hb.opencpu.org 
  ── 1. Error: echo large data (@test-echo.R#7)  ─────────────────────────────────
  Callback aborted
  1: curl::curl_echo(handle = handle) at testthat/test-echo.R:7
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 175 SKIPPED: 1 FAILED: 1
  1. Error: echo large data (@test-echo.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
'library' or 'require' call to ‘locfit’ which was already attached by Depends.
  Please remove these calls from your code.
Packages in Depends field not imported from:
  ‘R.methodsS3’ ‘R.oo’ ‘locfit’ ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
curvefit: no visible global function definition for ‘model.frame’
curvefit: no visible global function definition for ‘model.response’
curvefit: no visible global function definition for ‘model.matrix’
curvetest: no visible global function definition for ‘model.frame’
curvetest: no visible global function definition for ‘plot’
curvetest.raw: no visible global function definition for ‘pt’
curvetest.raw: no visible global function definition for ‘pnorm’
getoptimalalpha: no visible global function definition for ‘gcvplot’
getoptimalalpha: no visible global function definition for ‘plot’
lines.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘plot’
plot.curvefit: no visible global function definition for ‘lines’
plot.curvefit: no visible global function definition for ‘points’
Undefined global functions or variables:
  gcvplot lines model.frame model.matrix model.response plot pnorm
  points pt
Consider adding
  importFrom("graphics", "lines", "plot", "points")
  importFrom("stats", "model.frame", "model.matrix", "model.response",
             "pnorm", "pt")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    4.1Mb
    libs   1.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 177-179 (cycling_data_analysis.Rmd) 
Error: processing vignette 'cycling_data_analysis.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-38 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘Rglpk’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dartR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  iterator.cpp:138:17: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:12:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:30:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  iterator_functions.cpp:48:8: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DatABEL.Rcheck/00install.out’ for details.
get_temporary_file_name: no visible global function definition for
  ‘runif’
Undefined global functions or variables:
  runif
Consider adding
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.5Mb
    libs   3.0Mb
Packages required but not available: ‘RGtk2’ ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Data report generation is finished. Please wait while your output file is being rendered.
Quitting from lines 729-768 (extending_dataMaid.Rmd) 
Error: processing vignette 'extending_dataMaid.Rmd' failed with diagnostics:
pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-34 (get_started.Rmd) 
Error: processing vignette 'get_started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 57.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  55.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="./webshot2dd96169dbd5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot2dd96169dbd5.png': No such file or directory
Quitting from lines 512-515 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘gWidgetsRGtk2’
Package required but not available: ‘SDD’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
DrawAlphas: no visible global function definition for ‘rmultinom’
DrawClasses: no visible global function definition for ‘runif’
GetGammaNames: no visible global function definition for ‘combn’
GetLambdaNamesForItem: no visible global function definition for
  ‘combn’
SampleParameterEstimates: no visible global function definition for
  ‘rnorm’
plot,attribute.class-missing: no visible binding for global variable
  ‘attr.number’
plot,attribute.class-missing: no visible binding for global variable
  ‘mean.attr’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘attr.profile.number’
plot,attribute.profile.class-missing: no visible binding for global
  variable ‘mean.attr.profile’
summary,attribute.class: no visible binding for global variable ‘value’
summary,attribute.profile.class: no visible binding for global variable
  ‘max.class’
Undefined global functions or variables:
  attr.number attr.profile.number combn max.class mean.attr
  mean.attr.profile rmultinom rnorm runif value
Consider adding
  importFrom("stats", "rmultinom", "rnorm", "runif")
  importFrom("utils", "combn")
to your NAMESPACE file.
Running examples in ‘ddeploy-Ex.R’ failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Connection timed out after 10002 milliseconds
Calls: duke_deploy ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/debug.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
There are ::: calls to the package's namespace in its code. A package
  almost never needs to use ::: for its own objects:
  ‘debug.Recall’ ‘debug.eval’ ‘debug.eval.guts’ ‘debug.fun.name’
  ‘evaluator’ ‘find.debug.HQ’ ‘mvb.sys.on.exit’ ‘stepping’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: package 'dplyr' was built under R version 3.5.1

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union


Attaching package: 'gridExtra'

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

    combine

Quitting from lines 84-97 (MultiObjectiveDecisionAnalysisinR.Rmd) 
Error: processing vignette 'MultiObjectiveDecisionAnalysisinR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Joining, by = "key"
Joining, by = "key"
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 102-122 (sjukhus.Rmd) 
Error: processing vignette 'sjukhus.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘BSgenome’ ‘BSgenome.Hsapiens.UCSC.hg19’

Package suggested but not available for checking: ‘VariantAnnotation’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 60.8Mb
  sub-directories of 1Mb or more:
    libs  58.1Mb
Error in re-building vignettes:
  ...

    cutree

Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gplots'

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

    bluered, greenred

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

    lowess

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 931-933 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.6Mb
    help   1.4Mb
    libs   1.5Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Running ‘test-that.R’ [191s/202s]
Running the tests in ‘tests/test-that.R’ failed.
Last 13 lines of output:
  Loading required package: devtools
  <simpleError: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).>
  ── 1. Error: Package readme can be built  (@test-build-readme.R#8)  ────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: build_readme("testReadme") at testthat/test-build-readme.R:8
  2: callr::r(build, args = list(pkg_path = pkg$path, readme_path = readme_path, ... = ..., 
         quiet = quiet), show = TRUE, spinner = FALSE)
  3: get_result(output = out, options)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 42 SKIPPED: 11 FAILED: 1
  1. Error: Package readme can be built  (@test-build-readme.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 48.5Mb
  sub-directories of 1Mb or more:
    libs  48.1Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   9.6Mb
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages required but not available: ‘missMethyl’ ‘methylumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.5Mb
Error in globalVariables(c("C", "R", "key.row", "key.col", "label.row",  : 
  could not find function "globalVariables"
kf: no visible global function definition for ‘dbinom’
Undefined global functions or variables:
  dbinom
Consider adding
  importFrom("stats", "dbinom")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following hidden files and directories:
  .directory
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
distSegment: no visible global function definition for ‘dist’
distShape: no visible global function definition for ‘dist’
distTriangle: no visible global function definition for ‘dist’
exactHausdorff: no visible global function definition for ‘aggregate’
Undefined global functions or variables:
  aggregate dist
Consider adding
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘RobExtremes’
Curvature: no visible global function definition for ‘tail’
gen.rarefac.div: no visible global function definition for ‘sd’
plot.fitsingleMod: no visible global function definition for ‘points’
plot.fitsingleMod: no visible global function definition for ‘lines’
ref.area: no visible global function definition for ‘integrate’
simm: no visible global function definition for ‘integrate’
Undefined global functions or variables:
  integrate lines points sd tail
Consider adding
  importFrom("graphics", "lines", "points")
  importFrom("stats", "integrate", "sd")
  importFrom("utils", "tail")
to your NAMESPACE file.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
Package suggested but not available for checking: ‘FKF’
'library' or 'require' calls in package code:
  ‘FKF’ ‘dlm’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dlmodeler.extract: no visible global function definition for ‘qnorm’
dlmodeler.fit.MAD: no visible global function definition for ‘optim’
dlmodeler.fit.MAPE: no visible global function definition for ‘optim’
dlmodeler.fit.MLE: no visible global function definition for ‘optim’
dlmodeler.fit.MSE: no visible global function definition for ‘optim’
dlmodeler.fit.sigma : fit.fun: no visible global function definition
  for ‘var’
dlmodeler.fit.sigma: no visible global function definition for ‘optim’
dlmodeler.forecast: no visible global function definition for ‘qnorm’
Undefined global functions or variables:
  optim qnorm var
Consider adding
  importFrom("stats", "optim", "qnorm", "var")
to your NAMESPACE file.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   2.1Mb
    libs   3.5Mb
Package in Depends field not imported from: ‘magic’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   6.3Mb
Package unavailable to check Rd xrefs: ‘doMPI’
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
File ‘DPpackage/libs/DPpackage.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’,
      ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDDPdensity.o’, ‘LDDPsurvival.o’,
      ‘LDPDdoublyintsba.o’, ‘PSgamgam.o’, ‘PSgamgauss.o’,
      ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’, ‘ToolsLDTFP.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘DPdensityreg.o’, ‘LDBDPdensity.o’, ‘LDDPdensity.o’,
      ‘LDDPsurvival.o’, ‘LDPDdoublyintsba.o’, ‘LDTFPdensity.o’,
      ‘LDTFPglmmpois.o’, ‘LDTFPsurvival.o’, ‘PSgamgam.o’,
      ‘PSgamgauss.o’, ‘PSgamlogit.o’, ‘PSgampois.o’, ‘PSgamprob.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Found the following significant warnings:
  compnoreggilks.cpp:31:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compnoreggilks.cpp:90:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:32:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:88:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:150:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:207:10: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  compreggilks.cpp:380:8: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/DPWeibull.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/drugCombo.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
Using constraints: b = 1
Using constraints: b = 1
Running default monotherapy fitting. Note that if constraints are needed, run mono fitting manually first
Using constraints: b = 1
Using constraints: b = 1
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot100643a05274.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot100643a05274.png': No such file or directory
Quitting from lines 357-358 (userGuide.Rmd) 
Error: processing vignette 'userGuide.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    media       2.2Mb
    shinyapps   2.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.3Mb
dsCHECK: no visible global function definition for ‘na.omit’
dsFC: no visible global function definition for ‘cor’
dsMC: no visible global function definition for ‘cor’
plot.ds: no visible global function definition for ‘plot’
plot.ds: no visible global function definition for ‘par’
plot.ds: no visible global function definition for ‘points’
plot.ds: no visible global function definition for ‘text’
Undefined global functions or variables:
  cor na.omit par plot points text
Consider adding
  importFrom("graphics", "par", "plot", "points", "text")
  importFrom("stats", "cor", "na.omit")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/dvfBm.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘wmtsa’ which was already attached by Depends.
  Please remove these calls from your code.
Package in Depends field not imported from: ‘wmtsa’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
perturbFBM: warning in circFBM(n, H, plot = FALSE): partial argument
  match of 'plot' to 'plotfBm'
circFBM: no visible global function definition for ‘fft’
circFBM: no visible global function definition for ‘rnorm’
circFBM: no visible global function definition for ‘par’
circFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘filter’
dvFBM: no visible global function definition for ‘quantile’
dvFBM: no visible global function definition for ‘lm’
dvFBM: no visible global function definition for ‘plot’
dvFBM: no visible global function definition for ‘abline’
filt: no visible global function definition for ‘wavDaubechies’
perturbFBM: no visible global function definition for ‘rnorm’
perturbFBM: no visible global function definition for ‘rbinom’
perturbFBM: no visible global function definition for ‘par’
perturbFBM: no visible global function definition for ‘segments’
perturbFBM: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline fft filter lm par plot points quantile rbinom rnorm segments
  wavDaubechies
Consider adding
  importFrom("graphics", "abline", "par", "plot", "points", "segments")
  importFrom("stats", "fft", "filter", "lm", "quantile", "rbinom",
             "rnorm")
to your NAMESPACE file.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs  16.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   2.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
File ‘EBS/libs/EBS.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘GeneralFunctions.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    libs  58.0Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/egor.Rcheck/00install.out’ for details.
elmtrain.default: no visible global function definition for ‘runif’
elmtrain.formula: no visible global function definition for
  ‘model.frame’
elmtrain.formula: no visible global function definition for
  ‘model.matrix’
elmtrain.formula: no visible global function definition for
  ‘model.response’
predict.elmNN: no visible global function definition for ‘fitted’
predict.elmNN: no visible global function definition for ‘model.matrix’
print.elmNN: no visible global function definition for ‘head’
print.elmNN: no visible global function definition for ‘fitted’
randomMatrix: no visible global function definition for ‘runif’
Undefined global functions or variables:
  fitted head model.frame model.matrix model.response runif
Consider adding
  importFrom("stats", "fitted", "model.frame", "model.matrix",
             "model.response", "runif")
  importFrom("utils", "head")
to your NAMESPACE file.
Package required but not available: ‘iCheck’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
elrm: no visible global function definition for ‘write.table’
plot.elrm: no visible global function definition for ‘dev.new’
progress: no visible global function definition for ‘flush.console’
update.elrm: no visible global function definition for ‘write.table’
Undefined global functions or variables:
  dev.new flush.console write.table
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("utils", "flush.console", "write.table")
to your NAMESPACE file.
File ‘elrm/libs/elrm.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Objects: ‘binomMCMC.o’, ‘functions.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘binomMCMC.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘lumi’
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/embed.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/emIRT.Rcheck/00install.out’ for details.
Running examples in ‘EmiStatR-Ex.R’ failed
The error most likely occurred in:

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

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot54225f141465.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot54225f141465.png': No such file or directory
Quitting from lines 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 117-120 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiStats.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/EpiWeek.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Equalden.HD.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Error in re-building vignettes:
  ...
Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ften00081.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 13630 bytes (13 KB)
==================================================
downloaded 13 KB

Table ten00081 cached at /tmp/RtmpsI9cRw/eurostat/ten00081_date_code_TF.rds
trying URL 'https://ec.europa.eu/eurostat/estat-navtree-portlet-prod/BulkDownloadListing?sort=1&file=data%2Ftgs00026.tsv.gz'
Content type 'application/octet-stream;charset=UTF-8' length 5998 bytes
==================================================
downloaded 5998 bytes

Quitting from lines 338-370 (eurostat_tutorial.Rmd) 
Error: processing vignette 'eurostat_tutorial.Rmd' failed with diagnostics:
Recv failure: Connection reset by peer
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/eVenn.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Running examples in ‘evolqg-Ex.R’ failed
The error most likely occurred in:

> ### Name: LModularity
> ### Title: L Modularity
> ### Aliases: LModularity
> 
> ### ** Examples
> 
> # A modular matrix:
> modules = matrix(c(rep(c(1, 0, 0), each = 5),
+ rep(c(0, 1, 0), each = 5),
+ rep(c(0, 0, 1), each = 5)), 15)
> cor.hypot = CreateHypotMatrix(modules)[[4]]
> hypot.mask = matrix(as.logical(cor.hypot), 15, 15)
> mod.cor = matrix(NA, 15, 15)
> mod.cor[ hypot.mask] = runif(length(mod.cor[ hypot.mask]), 0.8, 0.9) # within-modules
> mod.cor[!hypot.mask] = runif(length(mod.cor[!hypot.mask]), 0.3, 0.4) # between-modules
> diag(mod.cor) = 1
> mod.cor = (mod.cor + t(mod.cor))/2 # correlation matrices should be symmetric
> 
> LModularity(mod.cor)
Error in method(g, ...) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Calls: LModularity -> method
Execution halted
Running ‘testthat.R’ [173s/275s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Loading required package: plyr
  ── 1. Error: LModularity resturn resonable results (@test.LModularity.r#12)  ───
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: expect_equal(modules, LModularity(mod.cor)[[2]]) at testthat/test.LModularity.r:12
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: LModularity(mod.cor)
  5: method(g, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 20953 SKIPPED: 1 FAILED: 1
  1. Error: LModularity resturn resonable results (@test.LModularity.r#12) 
  
  Error: testthat unit tests failed
  Execution halted
Packages in Depends field not imported from:
  ‘lars’ ‘ncvreg’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
plot.path: no visible global function definition for ‘par’
plot.path: no visible global function definition for ‘plot’
plot.path: no visible global function definition for ‘axis’
plot.path: no visible global function definition for ‘points’
plot.path: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline axis par plot points
Consider adding
  importFrom("graphics", "abline", "axis", "par", "plot", "points")
to your NAMESPACE file.
Running examples in ‘exampletestr-Ex.R’ failed
The error most likely occurred in:

> ### Name: make-test-shells
> ### Title: Create test shells.
> ### Aliases: make-test-shells make_test_shell_fun make_tests_shells_file
> ###   make_tests_shells_pkg
> 
> ### ** Examples
> 
> usethis::create_package(tempdir(), open = FALSE)
Error: '/tmp' is not a directory.
Execution halted
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  6: withVisible(eval(expr, pf))
  7: eval(expr, pf)
  8: eval(expr, pf)
  9: usethis::create_package(tempdir(), open = FALSE)
  10: create_directory(path_dir(path), name)
  11: stop_glue("{value(base_path)} is not a directory.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 13 SKIPPED: 0 FAILED: 3
  1. Error: `extract_examples()` works (@test-exemplar.R#7) 
  2. Error: `make_test_shell()` works (@test-exemplar.R#47) 
  3. Error: `make_tests_shell_fun()` works (@test-exemplar.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘exams-Ex.R’ failed
The error most likely occurred in:

> ### Name: exams2openolat
> ### Title: Generation of Exams for OpenOLAT
> ### Aliases: exams2openolat
> ### Keywords: utilities
> 
> ### ** Examples
> 
> ## load package and enforce par(ask = FALSE)
> library("exams")
> options(device.ask.default = FALSE)
> 
> ## define an exams (= list of exercises)
> myexam <- list(
+   "boxplots",
+   c("tstat", "ttest", "confint"),
+   c("regression", "anova"),
+   c("scatterplot", "boxhist"),
+   "relfreq"
+ )
> 
> ## output directory
> mydir <- tempdir()
> 
> ## generate .zip with OpenOLAT test in temporary directory
> exams2openolat(myexam, n = 3, dir = mydir)
Loading required namespace: rmarkdown
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    exiftool  12.8Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FACTscorer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fArma.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.9Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  15.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fastR2.Rcheck/00install.out’ for details.
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  16.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      4.9Mb
Found the following significant warnings:
  Rconnection.cc:347:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
  Rconnection.cc:356:12: warning: comparison of unsigned expression < 0 is always false [-Wtautological-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FastRWeb.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FateID.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   2.1Mb
Found the following significant warnings:
  fcnn/level2.cpp:82:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:119:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  fcnn/level2.cpp:165:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/FCNN4R.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs  32.5Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   5.5Mb
Running ‘test-as-dgCMatrix.R’ [3s/4s]
  Running ‘test-empty_array.R’ [3s/4s]
  Running ‘test-existence_collision.R’ [2s/4s]
  Running ‘test-hash.mapping.R’ [2s/4s]
  Running ‘test-hashing.R’ [3s/4s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fifer.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
plot.cf: no visible global function definition for ‘barplot’
plot.cf: no visible global function definition for ‘lines’
plot.cf: no visible global function definition for ‘abline’
plot.cf: no visible global function definition for ‘axis’
plot.cf: no visible global function definition for ‘curve’
plot.tvm: no visible global function definition for ‘barplot’
plot.tvm: no visible global function definition for ‘lines’
tvm: no visible global function definition for ‘uniroot’
update.tvm: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  abline axis barplot curve lines uniroot
Consider adding
  importFrom("graphics", "abline", "axis", "barplot", "curve", "lines")
  importFrom("stats", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/fingerPro.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning 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: Removed 2 rows containing missing values (geom_point).
Warning in normalizePath(f2) :
  path[1]="./webshot1672e13f906b7.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1672e13f906b7.png': No such file or directory
Quitting from lines 137-146 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 70-72 (lifeExpectancy.Rmd) 
Error: processing vignette 'lifeExpectancy.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 22-24 (fitbitScraper-examples.Rmd) 
Error: processing vignette 'fitbitScraper-examples.Rmd' failed with diagnostics:
login failed
Execution halted
Package suggested but not available for checking: ‘devEMF’
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
FlimFormula: no visible global function definition for ‘is’
FlimFormula: no visible global function definition for ‘terms’
FlimFormula: no visible global function definition for ‘reformulate’
ImputateMissingValues : RegFun: no visible global function definition
  for ‘lm’
ImputateMissingValues : RegFun: no visible binding for global variable
  ‘na.omit’
ImputateMissingValues: no visible global function definition for
  ‘predict’
ImputateMissingValues: no visible global function definition for
  ‘model.matrix’
ImputateMissingValues: no visible global function definition for ‘coef’
flimList: no visible global function definition for ‘coef’
flimSD: no visible binding for global variable ‘sd’
plot.flim: no visible global function definition for ‘plot’
plot.flim: no visible global function definition for ‘lines’
plot.flim: no visible global function definition for ‘points’
plot.flimList: no visible global function definition for ‘par’
plot.flimList: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘plot’
plot.flimboot: no visible global function definition for ‘points’
plot.flimboot: no visible global function definition for ‘lines’
spaplot: no visible global function definition for ‘plot’
spaplot: no visible global function definition for ‘lines’
Undefined global functions or variables:
  coef is lines lm model.matrix na.omit par plot points predict
  reformulate sd terms
Consider adding
  importFrom("graphics", "lines", "par", "plot", "points")
  importFrom("methods", "is")
  importFrom("stats", "coef", "lm", "model.matrix", "na.omit", "predict",
             "reformulate", "sd", "terms")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
error: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool: more than one input file specified (/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so.dSYM and /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/float.Rcheck/float/libs/float.so)
Usage: /Applications/Xcode.app/Contents/Developer/Toolchains/XcodeDefault.xctoolchain/usr/bin/install_name_tool [-change old new] ... [-rpath old new] ... [-add_rpath new] ... [-delete_rpath old] ... [-id name] input
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 38-49 (Using_fontHind.Rmd) 
Error: processing vignette 'Using_fontHind.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 56-67 (Using_fontMPlus.Rmd) 
Error: processing vignette 'Using_fontMPlus.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 168-169 (formattable-data-frame.Rmd) 
Error: processing vignette 'formattable-data-frame.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘Rsocp’ ‘Rnlminb2’ ‘Rdonlp2’ ‘Rsymphony’
Running examples in ‘FREddyPro-Ex.R’ failed
The error most likely occurred in:

> ### Name: buildTimestamp
> ### Title: Build a timestamp
> ### Aliases: buildTimestamp
> 
> ### ** Examples
> 
> ## Load the data
> data(fluxes)
> 
> ## Clean fluxes
> fluxes=cleanFluxes(fluxes,sdCor=TRUE,sdTimes=3,timesList=3,distCor=TRUE,
+                    thresholdList=list(H=c(-100,1000),LE=c(-100,1000)))	
> 
> ## Remove some line as an example
> fluxes=fluxes[-c(832,833,834,835,840,953),]
> 
> ## Create timestamp from date and time
> fluxes=createTimestamp(fluxes)
> 
> ## Now fill the gap timestmaps with NA's
> fluxes=fillTimestamp(fluxes,flux=TRUE)
[1] Discontinuity in 3 instances
[1] 2014-06-14 03:30:00 UTC 2014-06-14 06:00:00 UTC 2014-06-16 14:30:00 UTC
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: fillTimestamp ... shift_time -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
add.p.value.legend: no visible global function definition for ‘legend’
cat.freq.post: no visible global function definition for ‘quantile’
draw.signif.post.boxes: no visible global function definition for
  ‘polygon’
plot.freqMAP: no visible global function definition for ‘layout’
plot.freqMAP: no visible global function definition for ‘plot’
plot.freqMAP: no visible global function definition for ‘points’
plot.freqMAP: no visible global function definition for ‘lines’
plot.freqMAP: no visible global function definition for ‘abline’
plot.freqMAP: no visible global function definition for ‘axTicks’
posterior.comparison.freqMAP: no visible global function definition for
  ‘quantile’
rdirichlet: no visible global function definition for ‘rgamma’
Undefined global functions or variables:
  abline axTicks layout legend lines plot points polygon quantile
  rgamma
Consider adding
  importFrom("graphics", "abline", "axTicks", "layout", "legend",
             "lines", "plot", "points", "polygon")
  importFrom("stats", "quantile", "rgamma")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   8.8Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Package in Depends field not imported from: ‘genlasso’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
dualpathFusedX.mod: no visible global function definition for
  ‘graph.adjacency’
dualpathFusedX.mod: no visible global function definition for
  ‘clusters’
dualpathFusedX.mod: no visible global function definition for ‘ginv’
dualpathFusedX.mod: no visible global function definition for
  ‘subcomponent’
dualpathFusedX.mod: no visible global function definition for ‘rBind’
fpca.nonscore.cluster: no visible global function definition for
  ‘kmeans’
fpca.score.cluster: no visible global function definition for ‘kmeans’
gen.dcbm: no visible global function definition for ‘rbinom’
gen.sbm: no visible global function definition for ‘rbinom’
Undefined global functions or variables:
  clusters ginv graph.adjacency kmeans rBind rbinom subcomponent
Consider adding
  importFrom("stats", "kmeans", "rbinom")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 604-605 (futureheatwaves.Rmd) 
Error: processing vignette 'futureheatwaves.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GADMTools.Rcheck/00install.out’ for details.
GAPerm : pmxCrossover: no visible global function definition for
  ‘runif’
GAReal : twoPointsCrossover: no visible global function definition for
  ‘runif’
GAReal : blendCrossover: no visible global function definition for
  ‘runif’
GAReal : mutateNoise: no visible global function definition for ‘runif’
GAReal : initPopulation: no visible global function definition for
  ‘runif’
plot.GAPerm: no visible global function definition for ‘plot’
plot.GAPerm: no visible global function definition for ‘grid’
plot.GAPerm: no visible global function definition for ‘lines’
plot.GAPerm: no visible global function definition for ‘legend’
plot.GAReal: no visible global function definition for ‘plot’
plot.GAReal: no visible global function definition for ‘grid’
plot.GAReal: no visible global function definition for ‘lines’
plot.GAReal: no visible global function definition for ‘legend’
Undefined global functions or variables:
  grid legend lines plot runif
Consider adding
  importFrom("graphics", "grid", "legend", "lines", "plot")
  importFrom("stats", "runif")
to your NAMESPACE file.
Package which this enhances but not available for checking: ‘doMPI’
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   6.5Mb
installed size is 66.3Mb
  sub-directories of 1Mb or more:
    libs  65.9Mb
installed size is 52.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     49.6Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  13.9Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
Found the following significant warnings:
  cGetHCS.c:9:33: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  cIdentical.c:9:34: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gdmp.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘VariABEL’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GenABEL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.7Mb
Warning: no function found corresponding to methods exports from ‘GenABEL’ for: ‘show’

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

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

  Warning: 'cBind' is deprecated.
  Warning: 'rBind' is deprecated.
Deprecated functions may be defunct as soon as of the next release of
R.
See ?Deprecated.
Package required but not available: ‘ShortRead’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
timedelay.lm: no visible global function definition for ‘lm’
timedelay.lm: no visible global function definition for ‘AIC’
timedelay.lm: no visible global function definition for ‘pdf’
timedelay.lm: no visible global function definition for ‘x11’
timedelay.lm: no visible global function definition for ‘rainbow’
timedelay.lm: no visible global function definition for ‘title’
timedelay.lm: no visible global function definition for ‘lines’
timedelay.lm: no visible global function definition for ‘predict’
timedelay.lm: no visible global function definition for ‘points’
timedelay.lm: no visible global function definition for ‘legend’
timedelay.lm: no visible global function definition for ‘dev.off’
timedelay.univariate.lm: no visible global function definition for ‘lm’
timedelay.univariate.lm: no visible global function definition for
  ‘AIC’
ts.bspline: no visible global function definition for ‘lm’
ts.bspline: no visible global function definition for ‘predict’
Undefined global functions or variables:
  AIC dev.off legend lines lm pdf points predict rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "pdf", "rainbow", "x11")
  importFrom("graphics", "legend", "lines", "points", "title")
  importFrom("stats", "AIC", "lm", "predict")
to your NAMESPACE file.
checkrows: no visible global function definition for ‘rnorm’
cv.trendfilter: no visible binding for global variable ‘sd’
plot.cv.trendfilter: no visible global function definition for ‘plot’
plot.cv.trendfilter: no visible global function definition for ‘lines’
plot.cv.trendfilter: no visible global function definition for ‘points’
plot.cv.trendfilter: no visible global function definition for ‘legend’
plot.gcv.genlasso: no visible global function definition for ‘plot’
plot.gcv.genlasso: no visible global function definition for ‘points’
plot.genlasso: no visible global function definition for ‘par’
plot.genlasso: no visible global function definition for ‘rainbow’
plot.genlasso: no visible global function definition for ‘plot’
plot.genlasso: no visible global function definition for ‘matplot’
plot.genlasso: no visible global function definition for ‘abline’
plot.genlasso: no visible global function definition for ‘text’
plot.genlasso: no visible global function definition for ‘lines’
plot.trendfilter: no visible global function definition for ‘plot’
plot.trendfilter: no visible global function definition for ‘matplot’
predict.genlasso: no visible global function definition for ‘coef’
softthresh: no visible global function definition for ‘coef’
Undefined global functions or variables:
  abline coef legend lines matplot par plot points rainbow rnorm sd
  text
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "abline", "legend", "lines", "matplot", "par",
             "plot", "points", "text")
  importFrom("stats", "coef", "rnorm", "sd")
to your NAMESPACE file.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    exdata   5.0Mb
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'User_manual.tex' failed.
LaTeX errors:
! Package babel Error: Unknown option `USenglish'. Either you misspelled it
(babel)                or the language definition file USenglish.ldf was not fo
und.

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

See the babel package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Packages suggested but not available for checking: ‘KEGG.db’ ‘reactome.db’
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geoelectrics.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   3.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R         3.9Mb
    extdata   1.3Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geomorph.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/geo.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Unexported objects imported by ':::' calls:
  ‘maps:::makepoly’ ‘maps:::mapgetg’ ‘maps:::mapgetl’ ‘maps:::mapname’
  See the note in ?`:::` about the use of this operator.
Error in setClass("Extent", representation(xmin = "numeric", xmax = "numeric",  : 
  could not find function "setClass"
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gettingtothebottom.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
example.alpha: no visible global function definition for ‘rnorm’
example.quadratic.approx: no visible global function definition for
  ‘rnorm’
generate_nnm: no visible global function definition for ‘rnorm’
generate_nnm: no visible global function definition for ‘rgamma’
generate_nnm: no visible global function definition for ‘dnorm’
plot_nnm: no visible global function definition for ‘stack’
testmatrix: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  dnorm rgamma rnorm stack
Consider adding
  importFrom("stats", "dnorm", "rgamma", "rnorm")
  importFrom("utils", "stack")
to your NAMESPACE file.
Package suggested but not available for checking: ‘RGtk2’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 106-107 (IntroductionToGFD.Rmd) 
Error: processing vignette 'IntroductionToGFD.Rmd' failed with diagnostics:
there is no package called 'RGtk2'
Execution halted
Found the following significant warnings:
  FORCE_certify.c:116:15: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GFORCE.Rcheck/00install.out’ for details.
installed size is 14.5Mb
  sub-directories of 1Mb or more:
    libs  14.0Mb
Running examples in ‘GGEBiplotGUI-Ex.R’ failed
The error most likely occurred in:

> ### Name: GGEBiplot
> ### Title: GGEBiplotGUI: Interactive GGE Biplots in R
> ### Aliases: GGEBiplot
> 
> ### ** Examples
> 
> data(Ontario)
> GGEBiplot(Data = Ontario)
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: GGEBiplot -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
Loading required package: plyr
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 45-49 (ggPredict.Rmd) 
Error: processing vignette 'ggPredict.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'gglogo'

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

    fortify

Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Warning in grid.Call.graphics(C_text, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Garamond"
Quitting from lines 46-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
Execution halted
Error in re-building vignettes:
  ...
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "Source Sans Pro"
Quitting from lines 142-143 (using_ggmcmc.Rmd) 
Error: processing vignette 'using_ggmcmc.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ggraptR.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x1235f6579
#1  0x1235f5945
#2  0x7fff93ac4529
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Running ‘test-all.R’ [1s/3s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  8: git2r::fetch(gitrepo, name = "github", credentials = credentials)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 9 SKIPPED: 0 FAILED: 8
  1. Error: Install a single package (@test_install.R#8) 
  2. Error: Install a single package, removing old install (@test_install.R#14) 
  3. Error: Install a single package w/o vignettes (@test_install.R#19) 
  4. Error: Install from a branch (@test_install.R#25) 
  5. Error: Install from a commit ref (@test_install.R#36) 
  6. Error: Install from a tag (@test_install.R#42) 
  7. Error: Install from a pull request (@test_install.R#49) 
  8. Error: (unknown) (@test_internal.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Warning: no function found corresponding to methods exports from ‘giRaph’ for: ‘coerce’, ‘initialize’, ‘show’

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

Probably some imports need to be declared in the NAMESPACE file.
'library' or 'require' call to ‘mathgraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: ‘rtracklayer’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
installed size is 40.2Mb
  sub-directories of 1Mb or more:
    libs  39.9Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
Errors in running code in vignettes:
when running code in ‘openbugs.Rnw’
  ...
+     kResult = try(R2OpenBUGS::bugs(forBugs$ragged, inits = int2, 
+         model.file = "bym.txt", n.chain = 2, n.iter = .... [TRUNCATED] 

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

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

Attaching package: ‘R2jags’

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

    traceplot

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

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
installed size is 38.0Mb
  sub-directories of 1Mb or more:
    libs  37.4Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Rcpp

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

Waiting for profiling to be done...
trying deprecated constructor; please alert package maintainer
error occurred during calling the sampler; sampling not done
Quitting from lines 134-135 (spatial-glms.Rmd) 
Error: processing vignette 'spatial-glms.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
installed size is 40.3Mb
  sub-directories of 1Mb or more:
    libs  39.4Mb
installed size is 59.7Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/gnmf.Rcheck/00install.out’ for details.
File ‘gnmf/libs/gnmf.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘FactorMatrix.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘FactorMatrix.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (installation-and-authentication.Rmd) 
Error: processing vignette 'installation-and-authentication.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'intro.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPoM.Rcheck/00install.out’ for details.
Errors in running code in vignettes:
when running code in ‘GPPFourier.Rnw’
  ...
+     pch = 19, type = "b", xlab = "time", ylab = "GPP", xlim = as.POSIXct(c("2010-01-01 ..." ... [TRUNCATED] 

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

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

  When sourcing ‘GPPFourier.R’:
Error: figure margins too large
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/GPseq.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
calc_chisq_statistic: no visible global function definition for ‘dpois’
generalized_poisson_likelihood: no visible global function definition
  for ‘var’
perform_permutation_de: no visible binding for global variable ‘rbinom’
perform_permutation_de: no visible global function definition for ‘var’
perform_permutation_ds: no visible binding for global variable ‘rbinom’
perform_permutation_ds: no visible global function definition for ‘var’
Undefined global functions or variables:
  dpois rbinom var
Consider adding
  importFrom("stats", "dpois", "rbinom", "var")
to your NAMESPACE file.
installed size is 44.3Mb
  sub-directories of 1Mb or more:
    libs  41.7Mb
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    R  19.3Mb
Package in Depends field not imported from: ‘dismo’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Packages required but not available:
  ‘tximport’ ‘EnsDb.Hsapiens.v86’ ‘EnsDb.Rnorvegicus.v79’
  ‘EnsDb.Mmusculus.v79’ ‘org.Mm.eg.db’ ‘org.Rn.eg.db’ ‘GenomicFeatures’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Namespaces in Imports field not imported from:
  ‘assertthat’ ‘magrittr’ ‘readr’ ‘stringr’ ‘tibble’
  All declared Imports should be used.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 29372 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpjUDYzi/x13717e8f67458/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

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


Program received signal SIGTRAP: Trace/breakpoint trap.

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

Package suggested but not available for checking: ‘cairoDevice’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/h5.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-107 (retype.Rmd) 
Error: processing vignette 'retype.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
haplo.ccs: no visible global function definition for ‘terms’
haplo.ccs: no visible global function definition for ‘model.response’
haplo.ccs: no visible global function definition for ‘model.matrix’
haplo.ccs.fit: no visible global function definition for ‘glm’
haplo.ccs.fit: no visible global function definition for
  ‘quasibinomial’
haplo.ccs.fit: no visible binding for global variable ‘logit’
haplo.ccs.fit: no visible global function definition for ‘coef’
print.summary.haplo.ccs: no visible global function definition for ‘pt’
sandcov: no visible global function definition for ‘coef’
sandcov: no visible global function definition for ‘model.matrix’
sandcov: no visible global function definition for ‘residuals’
Undefined global functions or variables:
  coef glm logit model.matrix model.response pt quasibinomial residuals
  terms
Consider adding
  importFrom("stats", "coef", "glm", "model.matrix", "model.response",
             "pt", "quasibinomial", "residuals", "terms")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 335-344 (haplor-vignette.Rmd) 
Error: processing vignette 'haplor-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 122-128 (Basic_use.Rmd) 
Error: processing vignette 'Basic_use.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs  17.9Mb
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
Error in re-building vignettes:
  ...

    filter

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

    layout

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.15.2

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

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

Quitting from lines 88-90 (heatmaply.Rmd) 
Error: processing vignette 'heatmaply.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
plot.threshpt: no visible global function definition for ‘glm’
plot.threshpt: no visible global function definition for ‘predict’
plot.threshpt: no visible global function definition for ‘plot’
plot.threshpt: no visible global function definition for ‘lines’
plot.threshpt: no visible global function definition for ‘abline’
plot.threshpt: no visible global function definition for ‘points’
print.summary.threshpt: no visible global function definition for
  ‘printCoefmat’
threshpt: no visible global function definition for ‘as.formula’
threshpt: no visible global function definition for ‘glm’
threshpt: no visible global function definition for ‘vcov’
threshpt: no visible global function definition for ‘pnorm’
threshpt: no visible global function definition for ‘predict’
Undefined global functions or variables:
  abline as.formula glm lines plot pnorm points predict printCoefmat
  vcov
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "points")
  importFrom("stats", "as.formula", "glm", "pnorm", "predict",
             "printCoefmat", "vcov")
to your NAMESPACE file.
Packages required but not available: ‘rtracklayer’ ‘HiTC’

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

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

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

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

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

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

Quitting from lines 162-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/hypervolume.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   3.6Mb
Found the following significant warnings:
  IBDsim.c:27:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:39:20: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:54:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  IBDsim.c:61:10: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IBDsim.Rcheck/00install.out’ for details.
ConfigureIBHM : <anonymous>: no visible global function definition for
  ‘dnorm’
FindActiv: no visible global function definition for ‘sd’
OptimizeActivCMAES: no visible global function definition for ‘runif’
OptimizeActivNM: no visible global function definition for ‘optim’
OptimizeActivNM: no visible global function definition for ‘runif’
OptimizeAllParams : goal: no visible global function definition for
  ‘relist’
OptimizeAllParams: no visible global function definition for ‘optim’
OptimizeAllParams: no visible global function definition for ‘relist’
OptimizeAllWeights: no visible global function definition for ‘optim’
OptimizeScalCMAES: no visible global function definition for ‘runif’
OptimizeScalNM: no visible global function definition for ‘optim’
OptimizeScalNM: no visible global function definition for ‘runif’
OptimizeWeights: no visible global function definition for ‘optim’
TrainIBHM: no visible global function definition for ‘enableJIT’
ValidationSC : <anonymous>: no visible global function definition for
  ‘predict’
group.by.samplesPerDim: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘predict’
summary.IBHM: no visible global function definition for ‘sd’
summary.IBHM: no visible global function definition for ‘cor’
Undefined global functions or variables:
  cor dnorm enableJIT optim predict relist runif sd
Consider adding
  importFrom("stats", "cor", "dnorm", "optim", "predict", "runif", "sd")
  importFrom("utils", "relist")
to your NAMESPACE file.
Running ‘testthat.R’ [5s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Package Rglpk needed for this function to work. Please install it.
  1: calibration(data = data_ex2, marginMatrix = margins, colWeights = "poids", description = FALSE, 
         bounds = "min", method = "min") at testthat/test_calibration_small_dataset.R:127
  2: minBoundsCalib(Xs = matrixCal, d = weights, total = formattedMargins, q = rep(1, 
         nrow(matrixCal)), maxIter = maxIter, description = description, precisionBounds = precisionBounds, 
         forceSimplex = forceSimplex, forceBisection = forceBisection)
  3: solveMinBoundsCalib(Xs, d, total, q, maxIter, calibTolerance, description)
  4: stop("Package Rglpk needed for this function to work. Please install it.", call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 59 SKIPPED: 0 FAILED: 1
  1. Error: Calibration on minimum bounds checks out (@test_calibration_small_dataset.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    R     14.5Mb
    doc    5.1Mb
    libs   8.9Mb
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
Package suggested but not available for checking: ‘mixAK’
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.1Mb
installed size is 41.7Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs  37.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in .local(object, ...) :
  some chains had errors; consider specifying chains = 1 to debug
Quitting from lines 72-73 (Package_Introduction.Rmd) 
Error: processing vignette 'Package_Introduction.Rmd' failed with diagnostics:
object 'all_resid' not found
Execution halted
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  25.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IDTurtle.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/IFSPlot.Rcheck/00install.out’ for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  12.8Mb
installed size is 24.0Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     17.0Mb
Found the following significant warnings:
  IM4ECpp.cpp:24:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:24:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:54: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  IM4ECpp.cpp:33:65: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:25:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:35:73: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:24:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:59: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:67: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  imIM4ECpp.cpp:33:78: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Immigrate.Rcheck/00install.out’ for details.
Running examples in ‘iMRMC-Ex.R’ failed
The error most likely occurred in:

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

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

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x123592579
#1  0x123591945
#2  0x7fff93ac4529
Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Packages suggested but not available for checking: ‘MLP’ ‘a4Base’
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  24.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/intpoint.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
interior_point2d: no visible global function definition for ‘points’
random_problem: no visible global function definition for ‘runif’
show2d: no visible global function definition for ‘plot’
show2d: no visible global function definition for ‘abline’
show2d: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline plot points runif
Consider adding
  importFrom("graphics", "abline", "plot", "points")
  importFrom("stats", "runif")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Namespaces in Imports field not imported from:
  ‘coda’ ‘lattice’
  All declared Imports should be used.
Running examples in ‘IRATER-Ex.R’ failed
The error most likely occurred in:

> ### Name: clean.admb
> ### Title: delete IRATE (ADMB) run files
> ### Aliases: clean.admb clean.IRATE
> 
> ### ** Examples
> 
> example.setup <- IRATE.examples()
> new.setup <- new.setup.path <- example.setup[1] # select old IRATE setup to reparameterize
> print(new.setup) # print setup name to be run
[1] "HoenigNonMixing"
> old.setup.path <- system.file(paste0("IRATE.examples/",new.setup,".dat"), package = "IRATER")
> 
> system(paste("mkdir -p ",new.setup.path)) # create run folder for new setup
> system(paste("cp",old.setup.path, new.setup.path)) # copy old setup in new run folder
> setwd(new.setup.path)
> 
> run.IRATE(new.setup) # compile and run setup
sh: admb: command not found
Error in R2admb::compile_admb(setup.file, safe = safe, re = re, verbose = verbose,  : 
  base admb command failed: run setup_admb(), or check ADMB installation
Calls: run.IRATE -> <Anonymous>
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   4.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
Packages in Depends field not imported from:
  ‘MASS’ ‘nlme’ ‘survival’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
JointRegBC.default : f: no visible global function definition for
  ‘pnorm’
JointRegBC.default : f: no visible global function definition for
  ‘dnorm’
JointRegBC.default: no visible global function definition for ‘nlminb’
JointRegBC.default: no visible global function definition for ‘fdHess’
JointRegBC.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
Found the following significant warnings:
  jomo1clmmC.c:105:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo1clmmhrC.c:107:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmC.c:128:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomo2clmmhrC.c:132:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
  jomooprobitC.c:84:3: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/jomo.Rcheck/00install.out’ for details.
CoxFit : GetEstimate: no visible global function definition for ‘lm’
CoxFit : GetEstimate: no visible global function definition for ‘vcov’
CoxModel_Year: no visible global function definition for ‘model.frame’
CoxModel_Year: no visible global function definition for ‘model.matrix’
joinpoint: no visible global function definition for ‘as.formula’
joinpoint: no visible global function definition for ‘model.frame’
joinpoint: no visible global function definition for ‘model.matrix’
joinpoint : plot.surv: no visible global function definition for
  ‘predict’
joinpoint : plot.surv: no visible global function definition for ‘plot’
joinpoint : plot.surv: no visible global function definition for
  ‘lines’
joinpoint : plot.surv: no visible global function definition for
  ‘legend’
read.seerstat: no visible global function definition for ‘read.table’
Undefined global functions or variables:
  as.formula legend lines lm model.frame model.matrix plot predict
  read.table vcov
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "as.formula", "lm", "model.frame", "model.matrix",
             "predict", "vcov")
  importFrom("utils", "read.table")
to your NAMESPACE file.
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    libs  14.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   9.6Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kerasformula.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmc.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/kmcudaR.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 120-123 (copper_mining_2d.Rmd) 
Error: processing vignette 'copper_mining_2d.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.7Mb
Found the following significant warnings:
  W_gamma_Cpp.cpp:14:39: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/LambertW.Rcheck/00install.out’ for details.
installed size is 79.5Mb
  sub-directories of 1Mb or more:
    libs  78.2Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs          12.0Mb
    testdata       1.8Mb
    vignettedata   2.0Mb
Running ‘MASSch04.R’ [1s/1s]
Running the tests in ‘tests/MASSch04.R’ failed.
Complete output:
  > #-*- R -*-
  > 
  > ## Script from Fourth Edition of `Modern Applied Statistics with S'
  > 
  > # Chapter 4   Graphical Output
  > 
  > library(MASS)
  Error: package or namespace load failed for 'MASS' in gzfile(file, "rb"):
   cannot open the connection
  In addition: Warning message:
  In gzfile(file, "rb") :
    cannot open compressed file '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/MASS/data/Rdata.rdx', probable reason 'No such file or directory'
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 41-42 (Intro_to_lavaanPlot.Rmd) 
Error: processing vignette 'Intro_to_lavaanPlot.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package suggested but not available for checking: ‘rtracklayer’
get.cp: no visible global function definition for ‘cov’
heatmap: no visible global function definition for ‘image’
heatmap: no visible global function definition for ‘grey’
heatmap: no visible global function definition for ‘abline’
heatmap: no visible global function definition for ‘axis’
heatmap: no visible global function definition for ‘box’
ld_lasso: no visible global function definition for ‘cor’
ld_lasso_method: no visible global function definition for ‘pchisq’
plot_beta: no visible global function definition for ‘plot’
plot_beta: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘par’
plot_ldlasso: no visible global function definition for ‘plot’
plot_ldlasso: no visible global function definition for ‘lines’
plot_ldlasso: no visible global function definition for ‘points’
trace.plot: no visible global function definition for ‘plot’
trace.plot: no visible global function definition for ‘lines’
trace.plot: no visible global function definition for ‘points’
Undefined global functions or variables:
  abline axis box cor cov grey image lines par pchisq plot points
Consider adding
  importFrom("grDevices", "grey")
  importFrom("graphics", "abline", "axis", "box", "image", "lines",
             "par", "plot", "points")
  importFrom("stats", "cor", "cov", "pchisq")
to your NAMESPACE file.
chisqfit: no visible global function definition for ‘hist’
drawsample: no visible global function definition for ‘runif’
fitdistribution: no visible global function definition for ‘optimize’
fitdistribution: no visible global function definition for ‘var’
fthetacum: no visible global function definition for ‘integrate’
fthetaf: no visible global function definition for ‘dbeta’
plot.angledist: no visible global function definition for ‘hist’
plot.angledist: no visible global function definition for ‘curve’
plot.angledist: no visible global function definition for ‘box’
plot.angledistlist: no visible global function definition for ‘pdf’
plot.angledistlist: no visible global function definition for ‘dev.off’
Undefined global functions or variables:
  box curve dbeta dev.off hist integrate optimize pdf runif var
Consider adding
  importFrom("grDevices", "dev.off", "pdf")
  importFrom("graphics", "box", "curve", "hist")
  importFrom("stats", "dbeta", "integrate", "optimize", "runif", "var")
to your NAMESPACE file.
File ‘leaps/libs/leaps.so’:
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Object: ‘leaps.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.0Mb
LICurvature.default : f: no visible global function definition for
  ‘dnorm’
LICurvature.default: no visible global function definition for ‘nlminb’
LICurvature.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm ginv nlminb
Consider adding
  importFrom("stats", "dnorm", "nlminb")
to your NAMESPACE file.
Packages suggested but not available for checking: ‘gWidgetsRGtk2’ ‘RGtk2’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 272-273 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 109-112 (linkspotterVignette.Rmd) 
Error: processing vignette 'linkspotterVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘CAMERA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   8.4Mb
Found the following hidden files and directories:
  .DESCRIPTION.swo
These were most likely included in error. See section ‘Package
structure’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/liso.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘Iso’ ‘MASS’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
S3 methods shown with full name in documentation object 'seq.log':
  ‘seq.log’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.3Mb
    testdata   1.6Mb
mq.g.diagnostics : mq_missinggenotype_plot: no visible global function
  definition for ‘plot.missing’
Undefined global functions or variables:
  plot.missing
Running examples in ‘lmem.gwaser-Ex.R’ failed
The error most likely occurred in:

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

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

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

    Total markers:      811 
    No. markers:        117 147 153 48 113 101 132 
    Percent genotyped:  99.9 
    Genotypes (%):      AA:41.7  BB:58.3 
> 
> #Marker Quality
> 
> mq.g.diagnostics (crossobj=cross.data,I.threshold=0.1,
+              p.val=0.01,na.cutoff=0.1)
Error in plot.missing(crossobj) : could not find function "plot.missing"
Calls: mq.g.diagnostics -> mq_missinggenotype_plot
Execution halted
Package required and available but unsuitable version: ‘stats’

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

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

> ### Name: confusion_stat
> ### Title: Display confusion or classification matrix following logistic
> ###   regression using glm with binomial family.
> ### Aliases: confusion_stat
> ### Keywords: models
> 
> ### ** Examples
> 
> library(MASS)
> library(LOGIT)
> data(R84)
> R84$cage <- R84$age - mean(R84$age)
> R84$cdoc <- R84$docvis - mean(R84$docvis)
> mylogit <- glm(outwork ~ cdoc + female + kids + cage + factor(edlevel),
+ family=binomial, data=R84)
> mu <- predict(mylogit, type="response")
> cutpoint<-ROCtest(mylogit, fold=10, type="Sensitivity")$cut
> mu[mu>=cutpoint]<-1
> mu[mu<cutpoint]<-0
> confusion_stat(mu, R84$outwork)
Error: `data` and `reference` should be factors with the same levels.
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
Package suggested but not available for checking: ‘RDRToolbox’
Running ‘testthat.R’ [10s/55s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("loose.rock")
  ── 1. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/")` did not produce any warnings.
  
  ── 2. Failure: run.cache base.dir in folder that does not have access (@test-run
  `run.cache(sum, 1, 2, 3, 4, 5, show.message = FALSE, base.dir = "/daca")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 147 SKIPPED: 0 FAILED: 2
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#27) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#36) 
  
  Error: testthat unit tests failed
  Execution halted
S3 methods shown with full name in documentation object 'lqa':
  ‘lqa.update2’

S3 methods shown with full name in documentation object 'lqa.control':
  ‘lqa.control’

S3 methods shown with full name in documentation object 'plot.lqa':
  ‘plot.lqa’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 46.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  44.2Mb
Found the following significant warnings:
  ./pr_queue_k.h:103:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:89:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:91:5: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:108:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:109:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
  ./pr_queue.h:110:4: warning: 'register' storage class specifier is deprecated and incompatible with C++17 [-Wdeprecated-register]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ltsk.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.1Mb
LVMMCOR.default : f: no visible global function definition for ‘pnorm’
LVMMCOR.default : f: no visible global function definition for ‘dnorm’
LVMMCOR.default: no visible global function definition for ‘nlminb’
LVMMCOR.default: no visible global function definition for ‘fdHess’
LVMMCOR.default: no visible global function definition for ‘ginv’
Undefined global functions or variables:
  dnorm fdHess ginv nlminb pnorm
Consider adding
  importFrom("stats", "dnorm", "nlminb", "pnorm")
to your NAMESPACE file.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
installed size is 25.9Mb
  sub-directories of 1Mb or more:
    libs  25.6Mb
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  18.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MagneticMap.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages required but not available: ‘RGtk2’ ‘gWidgetsRGtk2’ ‘lumi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  14.1Mb
Error in re-building vignettes:
  ...
Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot1b95497e3633.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1b95497e3633.png': No such file or directory
Quitting from lines 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd023306255d6.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd023306255d6.png': No such file or directory
Quitting from lines 61-68 (manipulateWidgets.Rmd) 
Error: processing vignette 'manipulateWidgets.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$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: igraph

Attaching package: 'igraph'

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

    decompose, spectrum

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

    union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 57-64 (mapfuser.Rmd) 
Error: processing vignette 'mapfuser.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 95-100 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   6.8Mb
Package suggested but not available for checking: ‘ASGSCA’
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   6.1Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

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

Execution halted

... incomplete output.  Crash?
find.cb : plotit: no visible global function definition for ‘plot’
find.cb : plotit: no visible global function definition for ‘points’
find.cb : plotit: no visible global function definition for ‘title’
plot.MCbound: no visible global function definition for ‘par’
plot.MCbound: no visible global function definition for ‘plot’
plot.MCbound: no visible global function definition for ‘lines’
plot.MCbound: no visible global function definition for ‘points’
plot.MCbound: no visible global function definition for ‘axis’
plot.MCbound: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  axis lines mtext par plot points title
Consider adding
  importFrom("graphics", "axis", "lines", "mtext", "par", "plot",
             "points", "title")
to your NAMESPACE file.
installed size is 25.3Mb
  sub-directories of 1Mb or more:
    libs  24.2Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
mdr.3WS: no visible global function definition for ‘combn’
mdr.cv: no visible global function definition for ‘combn’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘combn’
permute.mdr : mdr.lrt: no visible global function definition for ‘glm’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘as.formula’
permute.mdr : mdr.lrt: no visible global function definition for
  ‘binomial’
permute.mdr : mdr.lrt: no visible binding for global variable ‘logit’
plot.mdr: no visible global function definition for ‘formula’
Undefined global functions or variables:
  as.formula binomial combn formula glm logit
Consider adding
  importFrom("stats", "as.formula", "binomial", "formula", "glm")
  importFrom("utils", "combn")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MDSMap.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   7.8Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: SKAT
Loading required package: pedgene
Loading required package: Matrix
Loading required package: CompQuadForm
Loading required package: survey
Loading required package: grid
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.4Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   3.6Mb
Packages suggested but not available for checking: ‘clpAPI’ ‘ctc’
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MetabolomicsBasics.Rcheck/00install.out’ for details.
Package required but not available: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 26-27 (MetaIntegrator.Rmd) 
Error: processing vignette 'MetaIntegrator.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Packages suggested but not available for checking:
  ‘annaffy’ ‘hgu133plus2.db’ ‘hgu133a.db’ ‘hgu95av2.db’
Packages suggested but not available for checking: ‘hgu133plus2.db’ ‘doSMP’
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...
    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


> library(HTSFilter)

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

Attaching package: ‘DESeq’

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

    estimateSizeFactorsForMatrix,
    getVarianceStabilizedData,
    varianceStabilizingTransformation


Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 9 (label = DESeq1study) 
Error in library(HTSFilter) : there is no package called ‘HTSFilter’
Execution halted
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.8Mb
Found the following significant warnings:
  binomial-twostage.cpp:78:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  binomial-twostage.cpp:280:4: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mets.Rcheck/00install.out’ for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.0Mb
    libs  14.1Mb
    misc   1.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: foreach
Loaded glmnet 2.0-16


Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mgcViz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘grasp2db’
installed size is 21.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  20.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 91-94 (mgwrsar-basic_examples.Rmd) 
Error: processing vignette 'mgwrsar-basic_examples.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Package suggested but not available for checking: ‘biotools’
Package unavailable to check Rd xrefs: ‘biotools’
Running examples in ‘micompr-Ex.R’ failed
The error most likely occurred in:

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Package suggested but not available for checking: ‘gWidgets2RGtk2’
Package suggested but not available for checking: ‘glpkAPI’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: Matrix
Loading required package: lattice
Quitting from lines 21-25 (MINVALintroduction.Rmd) 
Error: processing vignette 'MINVALintroduction.Rmd' failed with diagnostics:
there is no package called 'glpkAPI'
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.3Mb
Packages suggested but not available for checking: ‘mixAK’ ‘BRugs’
Package unavailable to check Rd xrefs: ‘mixAK’
Found the following significant warnings:
  simcensor.cpp:91:16: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:91:41: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
  simcensor.cpp:95:17: warning: result of comparison of constant 18446744073709551615 with expression of type 'unsigned int' is always true [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/missDeaths.Rcheck/00install.out’ for details.
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
npmlt: no visible global function definition for ‘model.frame’
npmlt: no visible binding for global variable ‘na.pass’
npmlt: no visible global function definition for ‘model.matrix’
npmlt: no visible global function definition for ‘na.omit’
npmlt: no visible global function definition for ‘glm’
npmlt: no visible binding for global variable ‘binomial’
npmlt: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  binomial cov2cor glm model.frame model.matrix na.omit na.pass
Consider adding
  importFrom("stats", "binomial", "cov2cor", "glm", "model.frame",
             "model.matrix", "na.omit", "na.pass")
to your NAMESPACE file.
Running examples in ‘MixSIAR-Ex.R’ failed
The error most likely occurred in:

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  ‘minfi’ ‘BiocStyle’ ‘wateRmelon’
  ‘IlluminaHumanMethylation450kmanifest’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-28 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
Error in re-building vignettes:
  ...
The following object is masked from 'package:variables':

    unit

Loading required package: RColorBrewer
Loading required package: mvtnorm
Loading required package: TH.data

Attaching package: 'TH.data'

The following object is masked from 'package:HSAUR3':

    birds

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

    geyser

trying URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Warning in download.file("https://zenodo.org/record/17179/files/DVC.tgz",  :
  cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz': HTTP status was '404 Not Found'
Quitting from lines 27-80 (mlt.Rnw) 
Error: processing vignette 'mlt.Rnw' failed with diagnostics:
cannot open URL 'https://zenodo.org/record/17179/files/DVC.tgz'
Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mlVAR.Rcheck/00install.out’ for details.
Running ‘testhat.R’ [18s/4s]
Running the tests in ‘tests/testhat.R’ failed.
Last 13 lines of output:
  Loading required package: mlvocab
  Loading required package: Rcpp
  Loading required package: Matrix
  Loading required package: digest
  Loading required package: sparsepp
  ── 1. Failure: vocab is computed correctly (@test_vocab.R#37)  ─────────────────
  `v` not equal to `vt`.
  Component "term": 7 string mismatches
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1199 SKIPPED: 0 FAILED: 1
  1. Failure: vocab is computed correctly (@test_vocab.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 33.5Mb
  sub-directories of 1Mb or more:
    libs  33.1Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Fbetaf.ct: no visible global function definition for ‘as’
Fbetaf.it: no visible global function definition for ‘as’
ci: no visible global function definition for ‘pnorm’
initial.values: no visible global function definition for ‘glm’
initial.values: no visible binding for global variable ‘binomial’
initial.values: no visible global function definition for ‘coef’
mseb: no visible global function definition for ‘rnorm’
mseb: no visible global function definition for ‘rmultinom’
msef.ct: no visible global function definition for ‘as’
msef.it: no visible global function definition for ‘as’
phi.direct: no visible global function definition for ‘as’
phi.direct.ct: no visible global function definition for ‘as’
phi.direct.it: no visible global function definition for ‘as’
Undefined global functions or variables:
  as binomial coef glm pnorm rmultinom rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "binomial", "coef", "glm", "pnorm", "rmultinom",
             "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mnreadR.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘MASS’ ‘parallel’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
dyld: Library not loaded: /Builds/unix/recipes/build/gdal-2.1.3-obj/libgdal.dylib
  Referenced from: /usr/local/bin/gdalinfo
  Reason: image not found
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   2.9Mb
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   5.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MortHump.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/mosaic.Rcheck/00install.out’ for details.
plot.Mposterior: no visible global function definition for ‘plot’
plot.Mposterior: no visible global function definition for ‘rainbow’
plot.Mposterior: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot rainbow
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "lines", "plot")
to your NAMESPACE file.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is 14.9Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  12.9Mb
File ‘MRwarping/libs/MRwarping.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘interfaceRC_warp.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Quitting from lines 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available: ‘mzR’ ‘xcms’

Depends: includes the non-default packages:
  ‘amap’ ‘clValid’ ‘cluster’ ‘fpc’ ‘mzR’ ‘xcms’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

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

Package suggested but not available for checking: ‘xcms’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
installed size is 43.3Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/msigdbr.Rcheck/00install.out’ for details.
Running examples in ‘mssqlR-Ex.R’ failed
Errors in running code in vignettes:
when running code in ‘chfls1.Rnw’
  ...

> library("xtable")

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

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

Error: processing vignette 'chfls1.Rnw' failed with diagnostics:
 chunk 1 (label = setup) 
Error : package or namespace load failed for ‘car’ in library.dynam(lib, package, package.lib):
 shared object ‘readxl.so’ not found
Execution halted
installed size is 59.6Mb
  sub-directories of 1Mb or more:
    libs  59.4Mb
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/MultiPhen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Undocumented S4 methods:
  generic '[<-' and siglist 'Multiplyr,ANY,ANY,ANY'
All user-level objects in a package (including S4 classes and methods)
should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: length_of_stay
> ### Title: Estimates length of stay
> ### Aliases: length_of_stay
> 
> ### ** Examples
> 
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'), 
+                status=c(NA, 'prstat', 'rfsstat'), 
+                data=ebmt3, 
+                trans=tmat, 
+                keep=c('age', 'dissub'))
>                
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> # New individual to estimate transition probabilities for
> newdata <- data.frame(age="20-40", dissub="AML")
> 
> # Estimate length of stay in each state after a year, given starting in state 1
> length_of_stay(models, 
+                newdata=newdata,
+                tmat, times=365.25,
+                start=1)

 *** caught illegal operation ***
address 0x103a76b00, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata_ext, tcovs, initial_times,     start_states, ci, M, agelimit, agecol, agescale)
 5: length_of_stay(models, newdata = newdata, tmat, times = 365.25,     start = 1)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [3s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  26: tryCatchList(expr, classes, parentenv, handlers)
  27: tryCatch(withCallingHandlers({    eval(code, test_env)    if (!handled && !is.null(test)) {        skip_empty()    }}, expectation = handle_expectation, skip = handle_skip, warning = handle_warning,     message = handle_message, error = handle_error), error = handle_fatal,     skip = function(e) {    })
  28: test_code(NULL, exprs, env)
  29: source_file(path, new.env(parent = env), chdir = TRUE, wrap = wrap)
  30: force(code)
  31: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        end_context()    })
  32: FUN(X[[i]], ...)
  33: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  34: force(code)
  35: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  36: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  37: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  38: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  39: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  41.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/nat.templatebrains.Rcheck/00install.out’ for details.
Warning: declared S3 method 'plot3d.templatebrain' not found
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 49-50 (using-nauf.Rmd) 
Error: processing vignette 'using-nauf.Rmd' failed with diagnostics:
Unable to extract deviance function from model fit
Execution halted
Errors in running code in vignettes:
when running code in ‘test-vignette.ipynbmeta’
  ...

  When tangling ‘test-vignette.ipynbmeta’:
Error: Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
Execution halted
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.9Mb
File ‘NeatMap/libs/NeatMap.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘nMDS_R.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘nMDS_R.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   4.5Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   4.6Mb
'library' or 'require' call to ‘igraph’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘Rcpp’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
File ‘NetSim/libs/NetSim.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘utils/Random.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘utils/Random.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages suggested but not available for checking:
  ‘BiocStyle’ ‘graphite’ ‘NFPdata’
Error in re-building vignettes:
  ...
Quitting from lines 10-11 (NFP.Rnw) 
Error: processing vignette 'NFP.Rnw' failed with diagnostics:
there is no package called 'BiocStyle'
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              6.5Mb
    classic-bugs   1.5Mb
    include        5.6Mb
    libs          18.6Mb
    tests          1.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-133 (geocode.Rmd) 
Error: processing vignette 'geocode.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   7.5Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/NNS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/novelist.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
delta.star: no visible global function definition for ‘cov’
delta.star: no visible global function definition for ‘cov2cor’
hardt: no visible global function definition for ‘cov2cor’
novelist.assign: no visible global function definition for ‘cov2cor’
novelist.assign.inv: no visible global function definition for
  ‘cov2cor’
novelist.cov.cv: no visible global function definition for ‘cov’
novelist.cov.cv: no visible global function definition for ‘cor’
novelist.inv.cv: no visible global function definition for ‘cov’
novelist.inv.cv: no visible global function definition for ‘cor’
softt: no visible global function definition for ‘cov2cor’
Undefined global functions or variables:
  cor cov cov2cor
Consider adding
  importFrom("stats", "cor", "cov", "cov2cor")
to your NAMESPACE file.
Found the following significant warnings:
  utilities.c:175:32: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/npcp.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘SweaveListingUtils’ ‘graphics’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
allsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for global variable ‘raw_data’
apsomv: no visible binding for '<<-' assignment to ‘NAwarning’
cfuinterpolation: no visible binding for global variable
  ‘measured_values’
cfuinterpolation: no visible global function definition for ‘lm’
cfuinterpolation: no visible global function definition for ‘coef’
disconestep: no visible global function definition for ‘runif’
disconestep: no visible binding for global variable ‘measured_values’
disconestep: no visible binding for global variable ‘psteps’
makepdfoutput: no visible binding for '<<-' assignment to ‘textt’
makepdfoutput: no visible global function definition for ‘Sweave’
npmpm: no visible binding for '<<-' assignment to ‘inputsettings’
npmpm: no visible binding for global variable ‘psteps’
npmpm: no visible binding for '<<-' assignment to ‘cfu’
npmpm: no visible binding for '<<-' assignment to ‘countwarnings’
npmpm: no visible binding for global variable ‘cfu’
onestep: no visible binding for global variable ‘measured_values’
onestep: no visible global function definition for ‘var’
onestep: no visible binding for global variable ‘psteps’
onestep: no visible global function definition for ‘rnorm’
psteppar: no visible global function definition for ‘runif’
simpleinterpolation: no visible binding for global variable
  ‘measured_values’
Undefined global functions or variables:
  Sweave cfu coef lm measured_values psteps raw_data rnorm runif var
Consider adding
  importFrom("stats", "coef", "lm", "rnorm", "runif", "var")
  importFrom("utils", "Sweave")
to your NAMESPACE file.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2Extras’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   7.9Mb
Error in re-building vignettes:
  ...
     
     taxi <- etl("nyctaxi", dir = "~/Desktop/nyctaxi/")
     taxi %>% 
        etl_extract(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_transform(years = 2016, months = 1:2, types = c("yellow","green")) %>% 
        etl_load(years = 2016, months = 1:2, types = c("yellow","green")) 
     ## End(Not run)
     


Attaching package: 'lubridate'

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

    date

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot16f9f6d730a2b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot16f9f6d730a2b.png': No such file or directory
Quitting from lines 61-71 (nyc_taxi.Rmd) 
Error: processing vignette 'nyc_taxi.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘obliclus/libs/obliclus.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘random_cluster_C.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘random_cluster_C.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    doc    1.5Mb
    help   2.5Mb
    libs   2.3Mb
installed size is 77.0Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Package in Depends field not imported from: ‘KMsurv’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
MLparameters: no visible global function definition for ‘optim’
comp.freq: no visible global function definition for ‘x11’
comp.freq: no visible global function definition for ‘par’
comp.freq: no visible global function definition for ‘plot’
Undefined global functions or variables:
  optim par plot x11
Consider adding
  importFrom("grDevices", "x11")
  importFrom("graphics", "par", "plot")
  importFrom("stats", "optim")
to your NAMESPACE file.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/OpenCL.Rcheck/00install.out’ for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.8Mb
installed size is 137.6Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    libs    127.6Mb
    models    4.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.7Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
Package suggested but not available for checking: ‘org.At.tair.db’
Running ‘bdstest.R’ [1s/1s]
  Running ‘hobbs.R’ [4s/4s]
Running the tests in ‘tests/hobbs.R’ failed.
Last 13 lines of output:
  In kktchk(ans$par, fn, wgr, hess = NULL, upper = NULL, lower = NULL,  :
    Eigenvalue failure for projected Hessian
  This problem is unconstrained.
  Error in lbfgsb3::lbfgsb3(prm = spar, fn = efn, gr = egr, control = mcontrol,  : 
    NA/NaN/Inf in foreign function call (arg 7)
  In addition: Warning messages:
  1: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  2: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  3: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  4: In nlm(f = nlmfn, p = spar, iterlim = iterlim, print.level = print.level,  :
    NA/Inf replaced by maximum positive value
  libc++abi.dylib: terminating with uncaught exception of type std::range_error: non-finite x values not allowed in calfun
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/optiSel.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.2Mb
Error in re-building vignettes:
  ...
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: processing vignette 'optparse.Rrst' failed with diagnostics:
pandoc document conversion failed with error 127
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
Ord.logreg: no visible binding for global variable ‘data’
plot.Ord.logreg: no visible global function definition for ‘par’
plot.Ord.logreg: no visible global function definition for ‘plot’
plot.Ord.logreg: no visible global function definition for ‘mtext’
plot.Ord.logreg: no visible global function definition for ‘plot.new’
Undefined global functions or variables:
  data mtext par plot plot.new
Consider adding
  importFrom("graphics", "mtext", "par", "plot", "plot.new")
  importFrom("utils", "data")
to your NAMESPACE file.
Package suggested but not available for checking: ‘IsoGene’
File ‘OriGen/libs/OriGen.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’

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

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

> ### Name: extract_id
> ### Title: Extract components from OSI metadata
> ### Aliases: extract_id extract_keywords extract_name extract_superseded
> ###   extractors
> 
> ### ** Examples
> 
> 
> #Get the names of all licenses
> all_license_metadata <- license_list()
Error in curl::curl_fetch_memory(url, handle = handle) : 
  Timeout was reached: Resolving timed out after 10005 milliseconds
Calls: license_list ... request_fetch -> request_fetch.write_memory -> <Anonymous>
Execution halted
Running ‘testthat.R’ [8s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  8: curl::curl_fetch_memory(url, handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 8
  1. Error: All licenses can be retrieved (@test_connectors.R#6) 
  2. Error: Keyword retrieval works (@test_connectors.R#14) 
  3. Error: ID retrieval works (@test_connectors.R#22) 
  4. Error: Content retrieval works (@test_connectors.R#29) 
  5. Error: licenses IDs can be retrieved (@test_extractors.R#4) 
  6. Error: licenses names can be retrieved (@test_extractors.R#11) 
  7. Error: licenses superseded states can be retrieved (@test_extractors.R#18) 
  8. Error: licenses keywords can be retrieved (@test_extractors.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   4.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 185-198 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages suggested but not available for checking:
  ‘genealogicalSorting’ ‘phybase’ ‘Rmpi’
Found the following significant warnings:
  Note: next used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PAactivPAL.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 196-217 (progressive_packing.Rmd) 
Error: processing vignette 'progressive_packing.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘ParallelForest/libs/ParallelForest.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘random_utils.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Object: ‘random_utils.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Downloading constituency data
Warning: Column `party_id` joining character vector and factor, coercing into character vector
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotc2552a92add0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotc2552a92add0.png': No such file or directory
Quitting from lines 67-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
File ‘parmigene/libs/parmigene.so’:
  Found ‘_rand_r’, possibly from ‘rand_r’ (C)
    Object: ‘points.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
pass: no visible global function definition for ‘predict’
plot.pass: no visible global function definition for ‘par’
plot.pass: no visible global function definition for ‘plot’
Undefined global functions or variables:
  par plot predict
Consider adding
  importFrom("graphics", "par", "plot")
  importFrom("stats", "predict")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Quitting from lines 58-63 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
Operation was aborted by an application callback
Execution halted
Packages suggested but not available for checking: ‘hu6800.db’ ‘golubEsets’

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

    union

Loading required package: lpSolve

> library(golubEsets)

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

    lowess

Loading required package: igraph

Attaching package: ‘igraph’

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

    normalize, path, union

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

    decompose, spectrum

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

    union

Loading required package: lpSolve

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package which this enhances but not available for checking: ‘pbdPROF’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pbdPROF.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pcaL1.Rcheck/00install.out’ for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.1Mb
    libs   6.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PCRedux.Rcheck/00install.out’ for details.
Package required but not available: ‘strvalidator’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    libs    5.7Mb
    share  11.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pdolsms.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Found the following significant warnings:
  spectrum.c:707:14: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:715:20: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1606:41: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  spectrum.c:1654:63: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Peaks.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pendensity.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/penRvine.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/permGPU.Rcheck/00install.out’ for details.
cdfDist: no visible global function definition for ‘tail’
cor2icc: no visible global function definition for ‘cor’
plot.cdfDist: no visible global function definition for ‘plot’
plot.cdfDist: no visible global function definition for ‘lines’
plot.cdfDist: no visible global function definition for ‘axis’
plot.cdfDist: no visible global function definition for ‘mtext’
plot.cdfDist: no visible global function definition for ‘legend’
Undefined global functions or variables:
  axis cor legend lines mtext plot tail
Consider adding
  importFrom("graphics", "axis", "legend", "lines", "mtext", "plot")
  importFrom("stats", "cor")
  importFrom("utils", "tail")
to your NAMESPACE file.
Namespaces in Imports field not imported from:
  ‘Rgraphviz’ ‘cluster’ ‘graph’
  All declared Imports should be used.
dvol.mse.est: no visible global function definition for ‘optim’
ellipsoidSurface: no visible global function definition for ‘integrate’
latscale: no visible global function definition for ‘uniroot’
covariogram,Segment-function: no visible global function definition for
  ‘integrate’
plot,FigLat-missing: no visible global function definition for ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘par’
plot,PointPattern-matrix: no visible global function definition for
  ‘lines’
plot,PointPattern-missing: no visible global function definition for
  ‘points’
plot,Quadrat-missing: no visible global function definition for ‘lines’
plot,Segment-matrix: no visible global function definition for ‘par’
plot,Segment-matrix: no visible global function definition for
  ‘polygon’
plot,Segment-missing: no visible global function definition for ‘lines’
Undefined global functions or variables:
  integrate lines optim par points polygon uniroot
Consider adding
  importFrom("graphics", "lines", "par", "points", "polygon")
  importFrom("stats", "integrate", "optim", "uniroot")
to your NAMESPACE file.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/phalen.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  LJMA_arms.c:297:11: warning: comparison of array 'env->p' equal to a null pointer is always false [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PhaseType.Rcheck/00install.out’ for details.
File ‘PhaseType/libs/PhaseType.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘LJMA_arms.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'Sample-scripts-external-genotype-simulation.Rmd' failed with diagnostics:
Failed to locate the ‘weave’ output file (by engine ‘knitr::rmarkdown’) for vignette with name ‘Sample-scripts-external-genotype-simulation’. The following files exist in directory ‘.’: ‘PhenotypeSimulator.R’, ‘PhenotypeSimulator.Rmd’, ‘PhenotypeSimulator.html’, ‘PhenotypeSimulator.md’, ‘Sample-scripts-external-genotype-simulation.Rmd’, ‘Sample-scripts-external-genotype-simulation.md’, ‘Simulation-and-LinearModel.Rmd’, ‘SimulationAndLinearModel.bib’, ‘genotype-simulation.bib’, ‘plos-genetics.csl’, ‘sample-scripts-external-genotype-simulation.html’
Execution halted
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    libs  19.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot19c9635f8145.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot19c9635f8145.png': No such file or directory
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Package required and available but unsuitable version: ‘phyloseq’

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.
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]="./webshot43b167d86d6c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot43b167d86d6c.png': No such file or directory
Quitting from lines 65-68 (v01-introduction.Rmd) 
Error: processing vignette 'v01-introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 24.1Mb
  sub-directories of 1Mb or more:
    libs  24.0Mb
Packages required but not available:
  ‘VariantAnnotation’ ‘Rsamtools’ ‘rtracklayer’

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

Package suggested but not available for checking: ‘latticist’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
dyld: Library not loaded: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib
  Referenced from: /Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libR.dylib
  Reason: no suitable image found.  Did find:
	/Library/Frameworks/R.framework/Versions/3.5/Resources/lib/libgfortran.3.dylib: pread of first 4K failed: 0
	/Library/Frameworks/R.framework/Resources/lib/libgfortran.3.dylib: file too short
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.9Mb
Packages required but not available: ‘pbdMPI’ ‘pbdBASE’ ‘pbdDMAT’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/pmlr.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
pmlr: no visible global function definition for ‘model.response’
pmlr: no visible global function definition for ‘model.matrix’
pmlr: no visible global function definition for ‘model.weights’
pmlr: no visible global function definition for ‘pchisq’
pmlr: no visible global function definition for ‘qnorm’
profileCIs: no visible global function definition for ‘qchisq’
test.LR: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  model.matrix model.response model.weights pchisq qchisq qnorm
Consider adding
  importFrom("stats", "model.matrix", "model.response", "model.weights",
             "pchisq", "qchisq", "qnorm")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
... activating corpus: germaparlmini
... activating corpus: reuters
Quitting from lines 139-140 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running examples in ‘PoloniexR-Ex.R’ failed
The error most likely occurred in:

> ### Name: ReturnTradeHistory,PoloniexPublicAPI-method
> ### Title: Returns the past 200 trades for a given market, or up to 50,000
> ###   trades inside a specified input date range interval.
> ### Aliases: ReturnTradeHistory,PoloniexPublicAPI-method
> 
> ### ** Examples
> 
> Sys.setenv(tz = "UTC")
> poloniex.public <- PoloniexPublicAPI()
> pair   <- "BTC_NXT"
> from   <- as.POSIXct("2017-07-04 00:00:00 UTC")
> to     <- as.POSIXct("2017-07-05 00:00:00 UTC")
> 
> trades.data <- ReturnTradeHistory(theObject = poloniex.public,
+                                   pair      = pair,
+                                   from      = from,
+                                   to        = to)
Error in .ProcessRequest(request.str) : 
  Unable to connect to https://poloniex.com/public?command=returnTradeHistory&currencyPair=BTC_NXT&start=1499140800&end=1499227200 (404)
Calls: ReturnTradeHistory -> ReturnTradeHistory -> .ProcessRequest
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/polyPK.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘Rsamtools’ ‘VariantAnnotation’ ‘GenomicFeatures’
Packages unavailable to check Rd xrefs: ‘Rsamtools’, ‘BSgenome’, ‘GenomicFeatures’, ‘VariantAnnotation’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 301-304 (polyRADtutorial.Rmd) 
Error: processing vignette 'polyRADtutorial.Rmd' failed with diagnostics:
there is no package called 'VariantAnnotation'
Execution halted
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘VariantAnnotation’
Errors in running code in vignettes:
when running code in ‘poplite.Rnw’
  ...
 8            8         8    18      0      1.68      0.535           2 F    
 9            9         9    20      1      0.911    -0.555           2 F    
10           10        10    12      1      0.237     1.78            1 M    
# ... with more rows

> library(VariantAnnotation)

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

    select

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

    filter

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

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

> suppressMessages(library(ROI))

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

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

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

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

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

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  ppcctest_pearson3.c:19:66: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ppcc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PPQplan.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning: Ignoring unknown aesthetics: z
Warning: Ignoring unknown aesthetics: z
Warning in normalizePath(f2) :
  path[1]="./webshot1635920dad531.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot1635920dad531.png': No such file or directory
Quitting from lines 125-126 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
Found the following significant warnings:
  ./shared.h:67:9: warning: result of comparison of constant 2147483648 with expression of type 'int' is always false [-Wtautological-constant-out-of-range-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/praznik.Rcheck/00install.out’ for details.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    libs  13.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 31-44 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 21.1Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PROFANCY.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
getCandidates: no visible binding for global variable ‘envData’
getGraph: no visible binding for global variable ‘envData’
getProvidedDiseaseName: no visible binding for global variable
  ‘envData’
getSeed: no visible binding for global variable ‘envData’
getTopDiseaseMetabolites: no visible binding for global variable
  ‘envData’
Undefined global functions or variables:
  envData
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      5.5Mb
Running examples in ‘ProFit-Ex.R’ failed
The error most likely occurred in:

> ### Name: profitConvolvePSF
> ### Title: High level image convolution
> ### Aliases: profitConvolvePSF
> ### Keywords: PSF convolve convolution
> 
> ### ** Examples
> 
> model = list(
+ 	sersic = list(
+ 		xcen   = c(180, 60),
+ 		ycen   = c(90, 10),
+ 		mag = c(15, 13),
+ 		re  = c(14, 5),
+ 		nser  = c(3, 10),
+ 		ang  = c(46, 80),
+ 		axrat  = c(0.4, 0.6),
+ 		box = c(0.5,-0.5)
+ 	)
+ )
> 
> model.image=profitMakeModel(model=model, dim=c(200,200))$z
> 
> psf=profitMakeGaussianPSF()
> 
> #Do some benchmarking:
> 
> temp=profitBenchmarkConv(model.image, psf=psf)

 *** caught segfault ***
address 0x60, cause 'memory not mapped'
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  ‘qtbase’ ‘RGtk2’ ‘cairoDevice’ ‘gWidgetsRGtk2’
Package suggested but not available for checking: ‘ALDEx2’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.8Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PsiHat.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Error in re-building vignettes:
  ...
The following object is masked from 'package:ggplot2':

    last_plot

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

    get_x, get_y

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

    filter

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

    layout

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]="./webshot6d9639cf936a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6d9639cf936a.png': No such file or directory
Quitting from lines 512-540 (bayesian.Rmd) 
Error: processing vignette 'bayesian.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  pinpolyhedronA.cc:594:7: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  pinpolyhedronA.cc:1766:5: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ptinpoly.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Running ‘testthat.R’ [54s/84s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    jurkat_06_100731121305
  Starting to work on MS/MS Peak shape ...
  
  Memory [MB] prior|after|max(diff) : 91.9 | 91.6 | 4204302 (4204210)
  
  Duration: 1 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 252 SKIPPED: 0 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#39) 
  2. Failure: createReport (@test_computeQC.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 34.2Mb
  sub-directories of 1Mb or more:
    libs  33.7Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PWFSLSmoke.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/PythonInR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QoLR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qpcR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  upwindorderedv4.c:542:54: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  upwindorderedv4.c:542:72: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/QPot.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/qtbase.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.7Mb
    doc       2.9Mb
    libs      1.3Mb
Package required but not available: ‘qtbase’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 92-106 (wilcox1973.Rmd) 
Error: processing vignette 'wilcox1973.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   9.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.2Mb
File ‘QUIC/libs/QUIC.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘QUIC.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘QUIC.o’

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

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

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
FancyPies: no visible global function definition for ‘rainbow’
FancyPies: no visible global function definition for ‘plot’
FancyPies: no visible global function definition for ‘polygon’
Hist2GE: no visible global function definition for ‘dist’
Pies2GE: no visible global function definition for ‘rainbow’
Plots2GE: no visible global function definition for ‘aggregate’
Plots2GE: no visible global function definition for ‘x11’
Plots2GE: no visible global function definition for ‘title’
Plots2GE: no visible global function definition for ‘png’
Plots2GE: no visible global function definition for ‘dev.off’
PolyLines2GE: no visible global function definition for ‘rainbow’
Shapes2GE: no visible global function definition for ‘rainbow’
Undefined global functions or variables:
  aggregate dev.off dist plot png polygon rainbow title x11
Consider adding
  importFrom("grDevices", "dev.off", "png", "rainbow", "x11")
  importFrom("graphics", "plot", "polygon", "title")
  importFrom("stats", "aggregate", "dist")
to your NAMESPACE file.
'library' or 'require' calls in package code:
  ‘RDCOMClient’ ‘rcom’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RaceID.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.basics.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.data.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.design.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.model.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.multivariate.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/radiant.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data      2.2Mb
    extdata   1.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    libs   4.2Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   9.2Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ramidst.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Package suggested but not available for checking: ‘Heatplus’
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs   3.9Mb
Packages required but not available: ‘Rsamtools’ ‘GenomicAlignments’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RAppArmor.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rpanel’
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs   5.5Mb
Running examples in ‘RAtmosphere-Ex.R’ failed
The error most likely occurred in:

> ### Encoding: UTF-8
> 
> ### Name: suncalc
> ### Title: Sunrise and Sunset calculations
> ### Aliases: suncalc
> ### Keywords: sun sunset sunrise
> 
> ### ** Examples
> 
> t<-Sys.time()+seq(-3600*12,3600*12,,by=600)
> t0=as.POSIXlt(Sys.time(),tz='UTC')
> plot(t,90-SZA(t,Lat=0,Lon=0),main='SZA',xlab='Time',ylab='El [°deg]')
> sun=suncalc(t0[['yday']],UTC=TRUE)
Error in FUN(X[[i]], ...) : subscript out of bounds
Calls: suncalc -> [[ -> [[.POSIXlt -> .POSIXlt -> lapply
Execution halted
Package suggested but not available for checking: ‘rattle’
Packages suggested but not available for checking:
  ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘playwith’ ‘rggobi’ ‘RGtk2’
  ‘RGtk2Extras’
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs  29.9Mb
Errors in running code in vignettes:
when running code in ‘rbiouml.Rnw’
  ...
filterExpression Expression in JavaScript like 'ColumnName1 > 5 && ColumnName2 < 0'
filteringMode                                                  Which rows to select
outputPath                                               Path to the filtered table

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

  When sourcing ‘rbiouml.R’:
Error: Internal server error: java.lang.NullPointerException
Execution halted
Error in re-building vignettes:
  ...
Loading required package: RCurl
Loading required package: bitops
Loading required package: RJSONIO
Warning in postForm(url, .params = params, .opts = opts, binary = binary) :
  No inputs passed to form

Error: processing vignette 'rbiouml.Rnw' failed with diagnostics:
 chunk 8 
Error in queryJSON("/web/analysis", params = c(jobID = jobID, de = analysisName,  : 
  Internal server error: java.lang.NullPointerException
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   4.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
Found the following executable file:
  src/vendor/clickhouse-cpp/contrib/lz4/LICENSE
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs  11.1Mb
Packages in Depends field not imported from:
  ‘Rcpp’ ‘RcppEigen’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Calls with DUP:
   .Call("hclust_from_distance", data = as.double(x), size = as.integer(attributes(x)$Size), 
       link = as.integer(method), DUP = FALSE, NAOK = FALSE, PACKAGE = "Rclusterpp")
   .Call("hclust_from_data", data = x, link = as.integer(method), 
       dist = as.integer(distance), p = as.numeric(p), DUP = FALSE, 
       NAOK = FALSE, PACKAGE = "Rclusterpp")
DUP is no longer supported and will be ignored.
Rclusterpp.package.skeleton: no visible global function definition for
  ‘packageDescription’
Undefined global functions or variables:
  packageDescription
Consider adding
  importFrom("utils", "packageDescription")
to your NAMESPACE file.
Found the following significant warnings:
  Warning: replacing previous import ‘Rcmdr::Confint’ by ‘car::Confint’ when loading ‘RcmdrPlugin.BCA’
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcmdrPlugin.BCA.Rcheck/00install.out’ for details.
.onAttach: no visible global function definition for ‘palette’
.onAttach: no visible global function definition for ‘dev.off’
helpAboutBCA: no visible global function definition for ‘help’
Undefined global functions or variables:
  dev.off help palette
Consider adding
  importFrom("grDevices", "dev.off", "palette")
  importFrom("utils", "help")
to your NAMESPACE file.
Packages 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.
Depends: includes the non-default packages:
  ‘Rcmdr’ ‘TeachingDemos’ ‘tseries’ ‘abind’ ‘MASS’ ‘xts’ ‘forecast’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'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.
Depends: includes the non-default packages:
  ‘Rcmdr’ ‘tcltk’ ‘car’ ‘RColorBrewer’ ‘colorspace’ ‘vcd’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
'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.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 62-65 (introducao-rcongresso.Rmd) 
Error: processing vignette 'introducao-rcongresso.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    corpora   7.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rcplex.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
    libs      1.7Mb
Found the following warnings:
  ../inst/include/blaze/math/smp/openmp/Functions.h:98:1: warning: control may reach end of non-void function [-Wreturn-type]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppBlaze.Rcheck/00install.out’ for details.
installed size is 27.2Mb
  sub-directories of 1Mb or more:
    include  25.3Mb
    libs      1.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppCWB.Rcheck/00install.out’ for details.
installed size is 31.2Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     23.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppMeCab.Rcheck/00install.out’ for details.
installed size is 34.5Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      24.0Mb
    libs      8.6Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   8.9Mb
    libs      2.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.2Mb
    libs      4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RcppRedis.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcqp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rcrypt.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
── Attaching packages ────────────────────────────────── tidyverse 1.2.1 ──
✔ ggplot2 2.2.1     ✔ purrr   0.2.4
✔ tibble  1.4.2     ✔ dplyr   0.7.4
✔ tidyr   0.8.0     ✔ stringr 1.3.0
✔ readr   1.1.1     ✔ forcats 0.3.0
── Conflicts ───────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()

Attaching package: 'jsonlite'

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

    flatten

Joining, by = "carrier"
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-40 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RDieHarder.Rcheck/00install.out’ for details.
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    libs   9.8Mb
Found the following significant warnings:
  dist.cpp:19:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:65:33: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
  dist.cpp:111:36: warning: explicitly assigning value of variable of type 'float' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rdist.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...

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

    set_names

SLF4J: Failed to load class "org.slf4j.impl.StaticLoggerBinder".
SLF4J: Defaulting to no-operation (NOP) logger implementation
SLF4J: See http://www.slf4j.org/codes.html#StaticLoggerBinder for further details.
WARNING: An illegal reflective access operation has occurred
WARNING: Illegal reflective access by com.thoughtworks.xstream.core.util.Fields (file:/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rdroolsjars/java/xstream-1.4.9.jar) to field java.util.TreeMap.comparator
WARNING: Please consider reporting this to the maintainers of com.thoughtworks.xstream.core.util.Fields
WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
WARNING: All illegal access operations will be denied in a future release
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning in normalizePath(f2) :
  path[1]="./webshot37525a7a3479.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot37525a7a3479.png': No such file or directory
Quitting from lines 374-381 (Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd) 
Error: processing vignette 'Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
checkForVServer: no visible global function definition for
  ‘download.file’
Undefined global functions or variables:
  download.file
Consider adding
  importFrom("utils", "download.file")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshotd14efb7b68.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotd14efb7b68.png': No such file or directory
Quitting from lines 22-26 (mapDWD.Rmd) 
Error: processing vignette 'mapDWD.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   6.4Mb
Package required but not available: ‘Rmosek’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   3.8Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  15.0Mb
HanoiTower: no visible global function definition for ‘object.size’
plot.HanoiTower: no visible global function definition for ‘plot’
plot.HanoiTower: no visible global function definition for ‘polygon’
plot.HanoiTower: no visible global function definition for ‘text’
Undefined global functions or variables:
  object.size plot polygon text
Consider adding
  importFrom("graphics", "plot", "polygon", "text")
  importFrom("utils", "object.size")
to your NAMESPACE file.
Package required but not available: ‘GenomeGraphs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/relax.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
'library' or 'require' call to ‘tkrplot’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘tcltk’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.2Mb
Found the following significant warnings:
  gar.c:356:29: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  gar.c:356:80: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/repeated.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: Testing the introduction presentation (@test-SlideDeck.R#5)  ──────
  Please install pandoc first: http://pandoc.org
  1: Read()$auto(fname, quiet = TRUE) at testthat/test-SlideDeck.R:5
  2: get(fileExt, mode = "function")(fileName, ...)
  3: md(mdFile)
  4: knitr::pandoc(fileName, format = "plain")
  5: stop("Please install pandoc first: http://pandoc.org")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error:  (@test-Evaluate.R#6) 
  2. Error: Testing the introduction presentation (@test-SlideDeck.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    java   5.8Mb
Running ‘testthat.R’ [3s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  13: ._jobjRef_dollar(x[["jobj"]], name)
  14: stop(sprintf("no field, method or inner class called '%s' ", name))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 4 SKIPPED: 0 FAILED: 7
  1. Error: (unknown) (@test-docx-bookmarks.R#4) 
  2. Error: (unknown) (@test-docx-img.R#8) 
  3. Error: (unknown) (@test-docx-plot.R#10) 
  4. Error: (unknown) (@test-file-extensions.R#3) 
  5. Error: (unknown) (@test-flextable.R#30) 
  6. Error: (unknown) (@test-pptx-img.R#9) 
  7. Error: (unknown) (@test-pptx-plot.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘restfulr_unit_tests.R’ [3m/28m]
Running the tests in ‘tests/restfulr_unit_tests.R’ failed.
Last 13 lines of output:
  > require("restfulr") || stop("unable to load restfulr package")
  Loading required package: restfulr
  [1] TRUE
  > restfulr:::.test()
  Loading required namespace: rsolr
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by org.xnio.nio.NioXnio$2 (file:/Users/urbanek/.local/share/R/rsolr/solr-undertow-1.5.0-RC1-with-solr-5.3.0/lib/xnio-nio-3.4.0.Beta1.jar) to constructor sun.nio.ch.KQueueSelectorProvider()
  WARNING: Please consider reporting this to the maintainers of org.xnio.nio.NioXnio$2
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  
  Execution halted
  rm: /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmprsxEQD: Too many open files
Packages suggested but not available for checking:
  ‘gWidgets2RGtk2’ ‘cairoDevice’ ‘RGtk2’
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/revengc.Rcheck/00install.out’ for details.
installed size is 28.1Mb
  sub-directories of 1Mb or more:
    libs  26.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 230-274 (rfm-customer-level-data.Rmd) 
Error: processing vignette 'rfm-customer-level-data.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    libs      77.3Mb
    pictures   1.3Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.4Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(rgeolocate)
  > 
  > test_check("rgeolocate")
  ── 1. Failure: non-existent files are detected (@test_maxmind.R#3)  ────────────
  `x` threw an error with unexpected message.
  Expected match: "could not be opened"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 51 SKIPPED: 0 FAILED: 1
  1. Failure: non-existent files are detected (@test_maxmind.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    3.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘gWidgetsRGtk2’ ‘hyperdraw’ ‘hypergraph’ ‘playwith’ ‘pmg’ ‘rggobi’
  ‘SVGAnnotation’
Running examples in ‘Rgretl-Ex.R’ failed
The error most likely occurred in:

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

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

Package suggested but not available for checking: ‘gWidgetsRGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RGtk2.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-47 (intro_rhandsontable.Rmd) 
Error: processing vignette 'intro_rhandsontable.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  filterhr.c:21:11: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:53: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  filterhr.c:21:95: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RHRV.Rcheck/00install.out’ for details.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
File ‘RInside/libs/RInside.so’:
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘RInside.o’
File ‘RInside/libs/RInside.so’:
  Found non-API calls to R: ‘R_CStackLimit’, ‘R_CleanTempDir’,
    ‘R_DefParams’, ‘R_ReplDLLdo1’, ‘R_ReplDLLinit’,
    ‘R_RunExitFinalizers’, ‘R_SetParams’, ‘R_SignalHandlers’,
    ‘R_TempDir’, ‘Rf_endEmbeddedR’, ‘Rf_initEmbeddedR’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rise.Rcheck/00install.out’ for details.
rite : 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.
Found the following significant warnings:
  Warning: The javah tool is planned to be removed in the next major
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rJava.Rcheck/rJava/libs/rJava.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
  Found ‘___stdoutp’, possibly from ‘stdout’ (C)
File ‘rJava/libs/rJava.so’:
  Found non-API call to R: ‘R_GlobalContext’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  libjson/Source/JSONSharedString.h:180:47: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  libjson/Source/JSONSharedString.h:182:66: warning: field 'len' will be initialized after field '_str' [-Wreorder]
  JSONStream.cpp:8:130: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:8:157: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  JSONStream.cpp:12:64: warning: field 'state' will be initialized after field 'call' [-Wreorder]
  JSONStream.cpp:12:100: warning: field 'err_call' will be initialized after field 'buffer' [-Wreorder]
  internalJSONNode.cpp:78:117: warning: field '_name_encoded' will be initialized after field '_name' [-Wreorder]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RJSONIO.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘golubEsets’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rLindo.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    libs   8.9Mb
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    rmd   6.8Mb
Found the following significant warnings:
  Warning: Software mark not found in path.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RMark.Rcheck/00install.out’ for details.
.onLoad: warning in dir(dll.path, pattern = this.ext, full = FALSE):
  partial argument match of 'full' to 'full.names'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[1], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: warning in apply(jumpDistRes, MARG = 2, FUN = quantile,
  probs = perc[2], na.rm = TRUE): partial argument match of 'MARG' to
  'MARGIN'
diagnos.envel: no visible global function definition for ‘quantile’
diagnos.envel: no visible global function definition for ‘qnorm’
diagnos.envel: no visible binding for global variable ‘quantile’
hrplot: no visible global function definition for ‘plot’
hrplot: no visible global function definition for ‘lines’
hrplot: no visible global function definition for ‘abline’
hrplot: no visible global function definition for ‘text’
sim.chain: no visible global function definition for ‘rnorm’
simRandWalk: no visible global function definition for ‘rnorm’
Undefined global functions or variables:
  abline lines plot qnorm quantile rnorm text
Consider adding
  importFrom("graphics", "abline", "lines", "plot", "text")
  importFrom("stats", "qnorm", "quantile", "rnorm")
to your NAMESPACE file.
File ‘RMC/libs/RMC.so’:
  Found ‘__ZNSt3__14coutE’, possibly from ‘std::cout’ (C++)
    Objects: ‘RMC.o’, ‘predict.o’
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘ap.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    libs  13.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.2Mb
dbGetDistinct,RMongo-character-character-character: no visible global
  function definition for ‘read.table’
dbGetQueryForKeys,RMongo-character-character-character-numeric-numeric:
  no visible global function definition for ‘read.csv’
Undefined global functions or variables:
  read.csv read.table
Consider adding
  importFrom("utils", "read.csv", "read.table")
to your NAMESPACE file.
Running examples in ‘RMongo-Ex.R’ failed
The error most likely occurred in:

> ### Name: dbAggregate-methods
> ### Title: Performing a MongoDB aggregate query
> ### Aliases: dbAggregate dbAggregate-methods
> ###   dbAggregate,RMongo,character,character-method
> 
> ### ** Examples
> 
>   mongo <- mongoDbConnect("test")
>   # insert two records
>   dbInsertDocument(mongo, "test_data", '{"foo": "bar", "size": 5 }')
Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
  com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
Calls: dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
Execution halted
Running ‘RMongo-Ex.R’ [4s/3s]
Running the tests in ‘tests/RMongo-Ex.R’ failed.
Last 13 lines of output:
  +   dbRemoveQuery(mongo, "test_data", '{}')
  +   dbDisconnect(mongo)
  +   
  +   # print(length(output))
  +   print(as.character(output[1]))
  + 
  +   checkEquals("{ \"_id\" : \"bar\"}", as.character(output[1]))
  +   # checkEquals("bar", as.character(output[1]))
  + }
  > 
  > test.dbInsertDocument()
  Error in .jcall(rmongo.object@javaMongo, "S", "dbInsertDocument", collection,  : 
    com.mongodb.MongoException$Network: Write operation to server /127.0.0.1:27017 failed on database test
  Calls: test.dbInsertDocument ... dbInsertDocument -> dbInsertDocument -> .jcall -> .jcheck
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmosek.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rmpi.Rcheck/00install.out’ for details.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs  10.7Mb
.isPath: no visible global function definition for ‘tail’
.isPath: no visible global function definition for ‘head’
navGraph : <anonymous>: no visible global function definition for
  ‘tail’
navGraph : <anonymous>: no visible global function definition for ‘sd’
navGraph: no visible global function definition for ‘colors’
ng_image_array_gray : <anonymous>: no visible global function
  definition for ‘grey’
scagGraph: no visible global function definition for ‘quantile’
closeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.off’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.new’
initializeViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.cur’
plot,NG_graph-ANY: no visible global function definition for ‘box’
plot,NG_graph-ANY: no visible global function definition for ‘axis’
plot,NG_graph-ANY: no visible global function definition for ‘points’
plot,NG_graph-ANY: no visible global function definition for ‘text’
plot,NG_graph-ANY: no visible global function definition for ‘segments’
updateViz,NG_Viz2DAxis: no visible global function definition for
  ‘dev.set’
Undefined global functions or variables:
  axis box colors dev.cur dev.new dev.off dev.set grey head points
  quantile sd segments tail text
Consider adding
  importFrom("grDevices", "colors", "dev.cur", "dev.new", "dev.off",
             "dev.set", "grey")
  importFrom("graphics", "axis", "box", "points", "segments", "text")
  importFrom("stats", "quantile", "sd")
  importFrom("utils", "head", "tail")
to your NAMESPACE file.
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doxygen   1.3Mb
    libs      3.3Mb
installed size is 94.7Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     92.6Mb
Packages required and available but unsuitable versions:
  ‘impute’ ‘MassSpecWavelet’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    libs  18.7Mb
Found the following significant warnings:
  ./hammock.h:369:15: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/robfilter.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  ‘affydata’ ‘hgu95av2cdf’ ‘beadarrayExampleData’ ‘illuminaHumanv3.db’
Package suggested but not available for checking: ‘SSOAP’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
installed size is 21.3Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.3Mb
Running examples in ‘robustX-Ex.R’ failed
The error most likely occurred in:

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

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

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

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

Package which this enhances but not available for checking: ‘ROI.plugin.cplex’
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    libs  18.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ROracle.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpanel.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rpg.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      3.8Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 51-53 (rpivotTableIntroduction.Rmd) 
Error: processing vignette 'rpivotTableIntroduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rpoppler.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  11: stringr::str_trim
  12: getExportedValue(pkg, name)
  13: asNamespace(ns)
  14: getNamespace(ns)
  15: tryCatch(loadNamespace(name), error = function(e) stop(e))
  16: tryCatchList(expr, classes, parentenv, handlers)
  17: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  18: value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 73 SKIPPED: 8 FAILED: 1
  1. Error: thisfile works with knitr (@test-thisfile.R#28) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'rprojroot.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  15.2Mb
Running ‘runUnitTests.R’ [2s/2s]
Running the tests in ‘tests/runUnitTests.R’ failed.
Last 13 lines of output:
  --------------------------- 
  Test file: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RProtoBuf.Rcheck/RProtoBuf/unitTests/runit.serialize_pb.R 
  test.serialize.sublist: (1 checks) ... OK (0.01 seconds)
  test.serialize_pb: (2 checks) ... OK (0.03 seconds)
  test.serialize_pb.alldatasets: (1 checks) ... OK (0.54 seconds)
  > 
  > ## Return success or failure to R CMD CHECK
  > if (getErrors(tests)$nFail > 0) {
  +    stop("TEST FAILED!")
  + }
  > if (getErrors(tests)$nErr > 0) {
  +    stop("TEST HAD ERRORS!")
  + }
  Error: TEST HAD ERRORS!
  Execution halted
'library' or 'require' calls to packages already attached by Depends:
  ‘RSAGA’ ‘shapefiles’
  Please remove these calls from your code.
Packages required but not available: ‘gWidgetsRGtk2’ ‘RGtk2’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RQuantLib.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/rrd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘biwavelet’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSAP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RSA.Rcheck/00install.out’ for details.
installed size is 22.0Mb
  sub-directories of 1Mb or more:
    dependencies  20.9Mb
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’

Package suggested but not available for checking: ‘ctc’

Depends: includes the non-default packages:
  ‘biwt’ ‘cairoDevice’ ‘fBasics’ ‘gplots’ ‘gWidgets’ ‘gWidgetsRGtk2’
  ‘minerva’ ‘parmigene’ ‘stringr’ ‘snowfall’
Adding so many packages to the search path is excessive and importing
selectively is preferable.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  11.7Mb
filterSD: no visible binding for global variable ‘sd’
filterSD: no visible global function definition for ‘quantile’
fit_lasso: no visible global function definition for ‘coef’
fit_prlasso: no visible global function definition for ‘coef’
rsig: no visible binding for global variable ‘mclapply’
rsig.all: no visible binding for global variable ‘mclapply’
rsig.all : <anonymous>: no visible global function definition for
  ‘flush.console’
rsig.all : <anonymous>: no visible global function definition for
  ‘predict’
Undefined global functions or variables:
  coef flush.console mclapply predict quantile sd
Consider adding
  importFrom("stats", "coef", "predict", "quantile", "sd")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
installed size is 15.7Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
installed size is 48.7Mb
  sub-directories of 1Mb or more:
    libs  48.2Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 112.5Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    doc     3.4Mb
    libs  107.1Mb
installed size is 230.5Mb
  sub-directories of 1Mb or more:
    libs  228.0Mb
Running ‘testthat.R’ [252s/415s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rstansim)
  Loading required package: Rcpp
  > 
  > test_check("rstansim")
  
   *** caught segfault ***
  address 0x107f89aa0, cause 'memory not mapped'
  
  Traceback:
   1: .Call(list(name = "CppObject__finalize", address = <pointer: 0x7fcf56212660>,     dll = list(name = "Rcpp", path = "/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/Rcpp/libs/Rcpp.so",         dynamicLookup = TRUE, handle = <pointer: 0x7fcf5620b0f0>,         info = <pointer: 0x7fcf5385df00>), numParameters = 2L),     <pointer: 0x7fcf53470440>, .pointer)
   2: x$.self$finalize()
   3: (function (x) x$.self$finalize())(<environment>)
  An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot14ab5585194ff.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot14ab5585194ff.png': No such file or directory
Quitting from lines 84-89 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.4Mb
Packages required but not available: ‘cairoDevice’ ‘gWidgetsRGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.8Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Running examples in ‘rviewgraph-Ex.R’ failed
The error most likely occurred in:

> ### Name: rViewGraph
> ### Title: This is a function to create and start the Java graph animation
> ###   GUI.
> ### Aliases: rViewGraph rViewGraph.default rViewGraph.Matrix
> ###   rViewGraph.igraph
> ### Keywords: graph
> 
> ### ** Examples
> 
> # 
> # Viewing an Erdos Renyui random graph specified by random edges.
> f = sample(100,size=200,replace=TRUE)
> t = sample(100,size=200,replace=TRUE)
> vft = rViewGraph(cbind(f,t))
Error in .jnew("rviewgraph/RViewGraph", v, f, t, x, y, directed, running) : 
  java.awt.HeadlessException
Calls: rViewGraph ... rViewGraph.default -> rViewGraphCore -> init -> .jnew
Execution halted
installed size is 46.7Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs     43.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RVowpalWabbit.Rcheck/00install.out’ for details.
S3 methods shown with full name in documentation object 'cbind.rv':
  ‘cbind.rv’ ‘rbind.rv’

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RWiener.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nchg.c:555:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/RxCEcolInf.Rcheck/00install.out’ for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs    6.3Mb
    yacas   1.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    sample_data   3.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SAENET.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
SAENET.nnet: no visible global function definition for ‘as.formula’
SAENET.nnet: no visible global function definition for ‘rnorm’
SAENET.train: no visible global function definition for ‘predict’
Undefined global functions or variables:
  as.formula predict rnorm
Consider adding
  importFrom("stats", "as.formula", "predict", "rnorm")
to your NAMESPACE file.
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SafeBayes.Rcheck/00install.out’ for details.
plot.safidesign: no visible global function definition for ‘par’
plot.safidesign: no visible global function definition for ‘matplot’
plot.safidesign: no visible global function definition for ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘colorRampPalette’
plot.safimodel : plot.coef: no visible global function definition for
  ‘barplot’
plot.safimodel : plot.coef: no visible global function definition for
  ‘axis’
plot.safimodel : plot.coef: no visible global function definition for
  ‘abline’
plot.safimodel : plot.coef: no visible global function definition for
  ‘box’
plot.safimodel: no visible global function definition for ‘par’
safiModel: no visible global function definition for ‘lm’
Undefined global functions or variables:
  abline axis barplot box colorRampPalette lm matplot par
Consider adding
  importFrom("grDevices", "colorRampPalette")
  importFrom("graphics", "abline", "axis", "barplot", "box", "matplot",
             "par")
  importFrom("stats", "lm")
to your NAMESPACE file.
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    libs  13.5Mb
Packages suggested but not available for checking:
  ‘mixer’ ‘networkTomography’ ‘org.Sc.sgd.db’
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 34-35 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  pointinpolygon.c:60:7: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  slope.aspect.c:128:33: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:50:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  vincenty.geodesics.c:126:13: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SDMTools.Rcheck/00install.out’ for details.
Found the following executable file:
  inst/external/env/bio14.bil
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sdStaf.Rcheck/00install.out’ for details.
Running ‘cran-tests.R’ [2s/2s]
Running the tests in ‘tests/cran-tests.R’ failed.
Last 13 lines of output:
  
  
  Program received signal SIGTRAP: Trace/breakpoint trap.
  
  Backtrace for this error:
  #0  0x1230e5579
  #1  0x1230e4945
  #2  0x7fff93ac4529
  Error: X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
  In addition: Warning messages:
  1: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4961ccbe9a/iofile -n -s 2>/dev/null' had status 133
  2: In system(paste(x13.bin, file, flags), intern = TRUE, ignore.stderr = TRUE) :
    running command '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//RtmpRVGyFB/x1313b4948f5a29f/iofile -n -s 2>/dev/null' had status 133
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.7Mb
Found the following significant warnings:
  BinNegative.cpp:108:5: warning: assigning field to itself [-Wself-assign-field]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/Segmentor3IsBack.Rcheck/00install.out’ for details.
Packages in Depends field not imported from:
  ‘datautils’ ‘irlba’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
computeKernel: no visible binding for global variable ‘sd’
computeKernel: no visible global function definition for ‘dist’
computeKernel: no visible global function definition for ‘quantile’
computeProjectionFromKernel : <anonymous>: no visible global function
  definition for ‘irlba’
distortions: no visible binding for global variable ‘sd’
distortions: no visible global function definition for ‘dist’
Undefined global functions or variables:
  dist irlba quantile sd
Consider adding
  importFrom("stats", "dist", "quantile", "sd")
to your NAMESPACE file.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.4Mb
Running examples in ‘seoR-Ex.R’ failed
The error most likely occurred in:

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   6.9Mb
Found the following significant warnings:
  vcf.c:253:15: warning: explicitly assigning value of variable of type 'int' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/seqminer.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
Packages suggested but not available for checking:
  ‘loomR’ ‘made4’ ‘SingleCellExperiment’ ‘MAST’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is 114.0Mb
  sub-directories of 1Mb or more:
    doc     11.8Mb
    libs    97.5Mb
    sqlite   1.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   9.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/shapes.Rcheck/00install.out’ for details.
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    www   6.4Mb
plot.intersect: no visible global function definition for ‘points’
plot.intersect: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘points’
plot.receiver: no visible global function definition for ‘plot’
plot.receiver: no visible global function definition for ‘segments’
plot.transmitter: no visible global function definition for ‘points’
plot.transmitter: no visible global function definition for ‘plot’
plot.transmitter: no visible global function definition for ‘lines’
Undefined global functions or variables:
  lines plot points segments
Consider adding
  importFrom("graphics", "lines", "plot", "points", "segments")
to your NAMESPACE file.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in normalizePath(f2) :
  path[1]="./webshot17b333efda763.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot17b333efda763.png': No such file or directory
Quitting from lines 26-42 (animate.Rmd) 
Error: processing vignette 'animate.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 89-90 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  10.5Mb
Package required but not available: ‘BSgenome’

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

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

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

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

Execution halted
plot.CorrAn : SAPplot: no visible global function definition for ‘plot’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘title’
plot.CorrAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.CorrAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.CorrAn: no visible global function definition for ‘dev.new’
plot.SimAn : SAPplot: no visible global function definition for ‘plot’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘title’
plot.SimAn : SAPtitle: no visible global function definition for
  ‘mtext’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘points’
plot.SimAn : SAPplotpuntos: no visible global function definition for
  ‘text’
plot.SimAn: no visible global function definition for ‘dev.new’
plot.SimAn: no visible global function definition for ‘points’
plot.SimAn: no visible global function definition for ‘text’
plot.SimAn: no visible global function definition for ‘par’
plot.SimAn: no visible global function definition for ‘plot’
plot.SimAn: no visible global function definition for ‘title’
plot.SimAn: no visible global function definition for ‘axis’
plot.SimAn: no visible global function definition for ‘arrows’
Undefined global functions or variables:
  arrows axis dev.new mtext par plot points text title
Consider adding
  importFrom("grDevices", "dev.new")
  importFrom("graphics", "arrows", "axis", "mtext", "par", "plot",
             "points", "text", "title")
to your NAMESPACE file.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    libs   4.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
plot.sla: no visible global function definition for ‘title’
plot.sla: no visible global function definition for ‘abline’
print.sla: no visible global function definition for ‘coef’
sla.default: no visible global function definition for ‘lm’
sla.default: no visible global function definition for ‘anova’
Undefined global functions or variables:
  abline anova coef lm title
Consider adding
  importFrom("graphics", "abline", "title")
  importFrom("stats", "anova", "coef", "lm")
to your NAMESPACE file.
Found the following significant warnings:
  MCP_efficient.c:114:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:134:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  MCP_efficient.c:154:16: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SMCP.Rcheck/00install.out’ for details.
'library' or 'require' calls in package code:
  ‘MASS’ ‘survival’
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   7.6Mb
Running examples in ‘sm-Ex.R’ failed
The error most likely occurred in:

> ### Name: sm.surface3d
> ### Title: Adding a regression surface to an rgl plot.
> ### Aliases: sm.surface3d
> ### Keywords: nonparametric regression smooth
> 
> ### ** Examples
> 
> with(trawl, {
+    Zone93    <- (Year == 1 & Zone == 1)
+    Position  <- cbind(Longitude - 143, Latitude)
+    model1 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.1, 0.1), display = "rgl", xlab="Longitude - 143")
+    model2 <- sm.regression(Position[Zone93,], Score1[Zone93],
+         h= c(0.2, 0.2), display = "none")
+    sm.surface3d(model2$eval.points, model2$est, model1$scaling, col = "red")
+ })
Error in sm.surface3d(model2$eval.points, model2$est, model1$scaling,  : 
  a scaling must be specified.
Calls: with -> with.default -> eval -> eval -> sm.surface3d
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SocialMediaLab.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
hsvScale: no visible global function definition for ‘hsv’
plotConcentric: no visible global function definition for ‘plot’
plotConcentric: no visible global function definition for ‘points’
plotConcentric: no visible global function definition for ‘legend’
plotPoints: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘plot’
plotStress: no visible global function definition for ‘polygon’
plotStress: no visible global function definition for ‘points’
Undefined global functions or variables:
  hsv legend plot points polygon
Consider adding
  importFrom("grDevices", "hsv")
  importFrom("graphics", "legend", "plot", "points", "polygon")
to your NAMESPACE file.
Packages in Depends field not imported from:
  ‘aqp’ ‘lattice’ ‘methods’ ‘munsell’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
'library' or 'require' call to ‘rgdal’ in package code.
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: ‘methods’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking:
  ‘r2cytoscape’ ‘BiocStyle’ ‘graphite’ ‘hgu95av2.db’
Packages unavailable to check Rd xrefs: ‘simPATHy’, ‘graphite’
Error in re-building vignettes:
  ...
    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.21 secs
Identifing all possible orderings..
Total run time: 0.86 secs
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshotf9064431846f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshotf9064431846f.png': No such file or directory
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spaceExt.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘glasso’ ‘limSolve’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
glasso.miss: no visible global function definition for ‘cov’
glasso.miss: no visible global function definition for ‘glasso’
glasso.miss: no visible global function definition for ‘Solve’
space.miss: no visible global function definition for ‘Solve’
Undefined global functions or variables:
  Solve cov glasso
Consider adding
  importFrom("stats", "cov")
to your NAMESPACE file.
Running ‘test-all.R’ [138s/212s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
    Using memoised copy of .inputObjects event in test module
    Using cached copy of .inputObjects event in test module. Adding to memoised copy.
  ── 1. Error: 3 levels of parent and child modules load and show correctly (@test
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
  1: moduleGraph(mySim, FALSE) at testthat/test-module-deps-methods.R:195
  2: moduleGraph(mySim, FALSE)
  3: cluster_optimal(grph)
  
    Using cached copy of .inputObjects event in child6 module. Adding to memoised copy.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 305 SKIPPED: 35 FAILED: 1
  1. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#195) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
    %>%


Attaching package: 'SpaDES.core'

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

    end, start

Loading required package: SpaDES.tools
Loading required package: RColorBrewer
Loading required package: raster
Loading required package: sp
Loading required package: grid

Attaching package: 'grid'

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

    gpar

Quitting from lines 366-372 (ii-modules.Rmd) 
Error: processing vignette 'ii-modules.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs  27.3Mb
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/spant.Rcheck/00install.out’ for details.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot10951185c772.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot10951185c772.png': No such file or directory
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘run-all.R’ [8s/35s]
Running the tests in ‘tests/run-all.R’ failed.
Last 13 lines of output:
  4: callJStatic("org.apache.spark.ml.r.GeneralizedLinearRegressionWrapper", "fit", formula, 
         data@sdf, tolower(family$family), family$link, tol, as.integer(maxIter), weightCol, 
         regParam, as.double(var.power), as.double(link.power), stringIndexerOrderType, 
         offsetCol)
  5: invokeJava(isStatic = TRUE, className, methodName, ...)
  6: handleErrors(returnStatus, conn)
  7: stop(readString(conn))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 2
  1. Error: create DataFrame from list or data.frame (@test_basic.R#26) 
  2. Error: spark.glm and predict (@test_basic.R#58) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
	at org.apache.spark.sql.Dataset.org$apache$spark$sql$Dataset$$collectFromPlan(Dataset.scala:3272)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$collect$1.apply(Dataset.scala:2722)
	at org.apache.spark.sql.Dataset$$anonfun$52.apply(Dataset.scala:3253)
	at org.apache.spark.sql.execution.SQLExecution$.withNewExecutionId(SQLExecution.scala:77)
	at org.apache.spark.sql.Dataset.withAction(Dataset.scala:3252)
	at org.apache.spark.sql.Dataset.collect(Dataset.scala:2722)
	at org.apache.spark.sql.api.r.SQLUtils$.dfToCols(SQLUtils.scala:173)
	at org.apache.spark.sql.api.r.SQLUtils.dfToCols(SQLUtils.scala)
	... 36 more
Quitting from lines 102-104 (sparkr-vignettes.Rmd) 
Error: processing vignette 'sparkr-vignettes.Rmd' failed with diagnostics:
java.lang.IllegalArgumentException
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.xbean.asm5.ClassReader.<init>(Unknown Source)
	at org.apache.spark.util.ClosureCleaner$.getClassReader(ClosureCleaner.scala:46)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:449)
	at org.apache.spark.util.FieldAccessFinder$$anon$3$$anonfun$visitMethodInsn$2.apply(ClosureCleaner.scala:432)
	at scala.collection.TraversableLike$WithFilter$$anonfun$foreach$1.apply(TraversableLike.scala:733)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashMap$$anon$1$$anonfun$foreach$2.apply(HashMap.scala:103)
	at scala.collection.mutable.HashTable$class.foreachEntry(HashTable.scala:230)
	at scala.collection.mutable.HashMap.foreachE
Execution halted
Package suggested but not available for checking: ‘RCy3’
Package unavailable to check Rd xrefs: ‘RCy3’
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 17.6Mb
  sub-directories of 1Mb or more:
    R      5.0Mb
    doc    4.8Mb
    help   5.1Mb
    libs   1.7Mb
installed size is 18.0Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
randomCorrelations: no visible global function definition for ‘cor’
specGlm : <anonymous>: no visible global function definition for ‘coef’
specLm : <anonymous>: no visible global function definition for ‘coef’
Undefined global functions or variables:
  coef cor
Consider adding
  importFrom("stats", "coef", "cor")
to your NAMESPACE file.
Packages required but not available: ‘xcms’ ‘MAIT’

Package suggested but not available for checking: ‘rcytoscapejs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: sp
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Warning in grid.Call(C_textBounds, as.graphicsAnnot(x$label), x$x, x$y,  :
  no font could be found for family "10"
Quitting from lines 45-64 (spew-quickstart.Rmd) 
Error: processing vignette 'spew-quickstart.Rmd' failed with diagnostics:
polygon edge not found
Execution halted
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.7Mb
Package suggested but not available for checking: ‘antaresViz’
Package unavailable to check Rd xrefs: ‘antaresViz’
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   6.5Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  12.0Mb
Running examples in ‘SRRS-Ex.R’ failed
The error most likely occurred in:

> ### Name: SRRS-package
> ### Title: The Stepwise Response Refinement Screener (SRRS)
> ### Aliases: SRRS-package
> 
> ### ** Examples
> 
> SRRS()
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: SRRS -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    include   9.5Mb
    lib       1.6Mb
Packages required but not available:
  ‘RGtk2’ ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RSCABS’

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

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


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

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

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

> WinHalfWidth<-30

> permReps<-10

> a<-maxchi(inputFile, breaks, WinHalfWidth, permReps)
Namespaces in Imports field not imported from:
  ‘lattice’ ‘xtable’
  All declared Imports should be used.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Packages in Depends field not imported from:
  ‘cubature’ ‘deldir’ ‘splancs’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
HRatio: no visible global function definition for ‘qnorm’
icweib: no visible global function definition for ‘model.frame’
icweib: no visible binding for global variable ‘na.pass’
icweib: no visible global function definition for ‘complete.cases’
icweib: no visible global function definition for ‘model.matrix’
icweib: no visible global function definition for ‘optim’
icweib: no visible global function definition for ‘pchisq’
icweib: no visible global function definition for ‘pnorm’
plot.icweib : getstat: no visible global function definition for
  ‘qnorm’
plot.icweib: no visible global function definition for ‘plot’
plot.icweib: no visible global function definition for ‘lines’
plot.icweib: no visible global function definition for ‘legend’
print.icweib: no visible global function definition for ‘pchisq’
Undefined global functions or variables:
  complete.cases legend lines model.frame model.matrix na.pass optim
  pchisq plot pnorm qnorm
Consider adding
  importFrom("graphics", "legend", "lines", "plot")
  importFrom("stats", "complete.cases", "model.frame", "model.matrix",
             "na.pass", "optim", "pchisq", "pnorm", "qnorm")
to your NAMESPACE file.
Found the following significant warnings:
  BIRCH/CFTree.cpp:18:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stream.Rcheck/00install.out’ for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.4Mb
installed size is 33.3Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package required but not available: ‘ShortRead’

Package suggested but not available for checking: ‘STRaitRazoR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
sh: line 1: 13800 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/x13ashtml /tmp/Rtmp3Fs7ok/x1335e058a2e03f/iofile -n -s 2> /dev/null
dyld: lazy symbol binding failed: Symbol not found: _mkostemp
  Referenced from: /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.5/x13binary/bin/../lib/libgfortran.3.dylib (which was built for Mac OS X 10.12)
  Expected in: /usr/lib/libSystem.B.dylib

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


Program received signal SIGTRAP: Trace/breakpoint trap.

Backtrace for this error:
#0  0x122fb2579
#1  0x122fb1945
#2  0x7fff93ac4529
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
X-13 has returned a non-zero exist status, which means that the current spec file cannot be processed for an unknown reason.
Execution halted
Packages required but not available: ‘gWidgets2RGtk2’ ‘RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/stUPscales.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SuppDists.Rcheck/00install.out’ for details.
Files named as vignettes but with no recognized vignette engine:
   ‘vignettes/copulas-concordance.tex’
   ‘vignettes/surrosurv.tex’
(Is a VignetteBuilder field missing?)
Packages required but not available: ‘clipper’ ‘qpgraph’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.4Mb
installed size is 81.6Mb
  sub-directories of 1Mb or more:
    libs  80.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
Found the following significant warnings:
  trlan/trlcore.c:983:15: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlcore.c:1642:9: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlcore.c:1642:20: warning: using floating point absolute value function 'fabs' when argument is of integer type [-Wabsolute-value]
  trlan/trlaux.c:28:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:41:13: warning: comparison of array 'info->log_file' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlaux.c:62:13: warning: comparison of array 'info->cpfile' not equal to a null pointer is always true [-Wtautological-pointer-compare]
  trlan/trlan.c:171:20: warning: comparison of array 'info->oldcpf' equal to a null pointer is always false [-Wtautological-pointer-compare]
  trlan/ztrlcore.c:1418:12: warning: comparison of array 'info->oldcpf' not equal to a null pointer is always true [-Wtautological-pointer-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/svd.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘svHttp’
File ‘svmpath/libs/svmpath.so’:
  Found ‘__gfortran_st_close’, possibly from ‘close’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_open’, possibly from ‘open’ (Fortran)
    Object: ‘mi10unix.o’
  Found ‘__gfortran_st_read’, possibly from ‘read’ (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi30spec.o’, ‘mi35mps.o’,
      ‘mi36mps.o’, ‘mi40bfil.o’
  Found ‘__gfortran_st_write’, possibly from ‘write’ (Fortran), ‘print’
    (Fortran)
    Objects: ‘mi02lib.o’, ‘mi05funs.o’, ‘mi10unix.o’, ‘mi11sys.o’,
      ‘mi12solv.o’, ‘mi20amat.o’, ‘mi25bfac.o’, ‘mi26bfac.o’,
      ‘mi27lu.o’, ‘mi30spec.o’, ‘mi35mps.o’, ‘mi36mps.o’, ‘mi40bfil.o’,
      ‘mi50lp.o’, ‘mi60srch.o’, ‘mi65rmod.o’, ‘mi70nobj.o’,
      ‘mi80ncon.o’, ‘mi81ncon.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  Warning: CHARACTER expression will be truncated in assignment (10/13) at (1) [-Wcharacter-truncation]
  Warning: ‘pst_kg’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘burn_frlb’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘hi_ovr’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘harveff’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘frac_harvk’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘lai_init’ is used uninitialized in this function [-Wuninitialized]
  Warning: ‘orig_tnylda’ is used uninitialized in this function [-Wuninitialized]
  Warning: CHARACTER expression will be truncated in assignment (1/3) at (1) [-Wcharacter-truncation]
  Warning: ‘fr_curb’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SWATmodel.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: ‘cplexAPI’ ‘glpkAPI’
Running examples in ‘sybilcycleFreeFlux-Ex.R’ failed
The error most likely occurred in:

> ### Name: cfFBA
> ### Title: cycle free flux
> ### Aliases: cfFBA lrFBA
> ### Keywords: cycle free flux loopless FBA
> 
> ### ** Examples
> 
> ##---- Should be DIRECTLY executable !! ----
> ##-- ==>  Define data, use random,
> ##--	or do  help(data=index)  for the standard data sets.
> data(iAF1260)
> model=iAF1260
> fba=optimizeProb(model)
Loading required package: glpkAPI
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘glpkAPI’
Error in checkDefaultMethod(solver, method, pType) : 
  package ‘glpkAPI’ not found
Calls: optimizeProb -> optimizeProb -> .local -> sysBiolAlg
Execution halted
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/sybilEFBA.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
FECorr: no visible global function definition for ‘is’
FECorr: no visible global function definition for ‘write.csv’
FECorr: no visible global function definition for ‘aggregate’
FECorr: no visible global function definition for ‘lm’
FECorr: no visible global function definition for ‘nlm’
eFBA_gene: no visible global function definition for ‘is’
eFBA_gene: no visible global function definition for ‘as’
eFBA_rxn : adjustTol: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘is’
eFBA_rxn: no visible global function definition for ‘as’
findFluxGeneExpr: no visible global function definition for ‘as’
findMDCFlux: no visible global function definition for ‘is’
findMDCFlux: no visible global function definition for ‘as’
gene2Rule: no visible global function definition for ‘is’
Undefined global functions or variables:
  aggregate as is lm nlm write.csv
Consider adding
  importFrom("methods", "as", "is")
  importFrom("stats", "aggregate", "lm", "nlm")
  importFrom("utils", "write.csv")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Packages suggested but not available for checking: ‘cplexAPI’ ‘clpAPI’
Found the following significant warnings:
  Note: break used in wrong context: no loop is visible 
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/SynergizeR.Rcheck/00install.out’ for details.
Information on the location(s) of code generating the ‘Note’s can be
obtained by re-running with environment variable R_KEEP_PKG_SOURCE set
to ‘yes’.
Packages in Depends field not imported from:
  ‘RCurl’ ‘RJSONIO’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   3.4Mb
Running ‘testthat.R’ [13s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Component 11: Modes: character, numeric
  Component 11: Lengths: 1, 3
  Component 11: names for current but not for target
  Component 11: target is character, current is numeric
  ...
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 4
  1. Failure: COX (@test_COX.R#6) 
  2. Failure: HTC (@test_HTC.R#6) 
  3. Failure: ITC (@test_ITC.R#6) 
  4. Failure: PTC (@test_PTC.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tcR.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.4Mb
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  12.0Mb
Namespaces in Imports field not imported from:
  ‘nlme’ ‘tidyr’
  All declared Imports should be used.
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
Depends: includes the non-default packages:
  ‘grid’ ‘quadprog’ ‘maps’ ‘maptools’ ‘mapdata’ ‘dichromat’
Adding so many packages to the search path is excessive and importing
selectively is preferable.
Packages in Depends field not imported from:
  ‘dichromat’ ‘grid’ ‘mapdata’ ‘maps’ ‘maptools’ ‘quadprog’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
installed size is 39.2Mb
  sub-directories of 1Mb or more:
    libs       7.2Mb
    tessdata  31.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.2Mb
installed size is 14.2Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
.dea_create_model: no visible global function definition for
  ‘getSrcFilename’
.wMean: no visible global function definition for ‘weighted.mean’
Undefined global functions or variables:
  getSrcFilename weighted.mean
Consider adding
  importFrom("stats", "weighted.mean")
  importFrom("utils", "getSrcFilename")
to your NAMESPACE file.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    rda    7.0Mb
Running examples in ‘threejs-Ex.R’ failed
The error most likely occurred in:

> ### Name: graphjs
> ### Title: Interactive 3D Graph Visualization
> ### Aliases: graphjs
> 
> ### ** Examples
> 
> set.seed(1)
> g <- sample_islands(3, 10, 5/10, 1)
> i <- cluster_optimal(g)
Error in cluster_optimal(g) : 
  At optimal_modularity.c:85 : GLPK is not available, Unimplemented function call
Execution halted
Running ‘testthat.R’ [6s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  14: mutate_as_tbl(.data, !!!dot)
  15: mutate(d_tmp, ...)
  16: mutate.tbl_df(d_tmp, ...)
  17: mutate_impl(.data, dots)
  18: group_optimal()
  19: membership(cluster_optimal(graph = .G(), weights = weights))
  20: cluster_optimal(graph = .G(), weights = weights)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 268 SKIPPED: 0 FAILED: 2
  1. Error: grouping returns integer vector (@test-group.R#14) 
  2. Error: grouping returns integer of correct length (@test-group.R#31) 
  
  Error: testthat unit tests failed
  Execution halted
Namespaces in Imports field not imported from:
  ‘tibble’ ‘tidyverse’
  All declared Imports should be used.
Running ‘testthat.R’ [2s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !!enquo(X), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !!!quos(...))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tidymodels.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
File ‘tidyxl/libs/tidyxl.so’:
  Found ‘_abort’, possibly from ‘abort’ (C)
    Object: ‘xlex.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

sh: sysctl: command not found
Quitting from lines 107-109 (Tigger-Vignette.Rmd) 
Error: processing vignette 'Tigger-Vignette.Rmd' failed with diagnostics:
error in running command
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 2015-01-01 23:56:02 - 2015-01-01 == 23.9 hours
  
  ── 3. Failure: updates on ydas works correctly with leap year (@test-update.R#17
  time_update(...) not equal to ymd("2016-01-10", tz = "America/New_York").
  1/1 mismatches
  [1] 2016-01-10 23:56:02 - 2016-01-10 == 23.9 hours
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 685 SKIPPED: 0 FAILED: 3
  1. Failure: updates on ydas works correctly with leap year (@test-update.R#173) 
  2. Failure: updates on ydas works correctly with leap year (@test-update.R#175) 
  3. Failure: updates on ydas works correctly with leap year (@test-update.R#177) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  tm.c:184:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  tm.c:185:9: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TimeMachine.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/tkrplot.Rcheck/00install.out’ for details.
Warning: loading Rplot failed

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

Probably some imports need to be declared in the NAMESPACE file.
Error in re-building vignettes:
  ...
Warning 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.
Linking to GEOS 3.6.1, GDAL 2.1.3, proj.4 4.9.3
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 127-131 (tmap-getstarted.Rmd) 
Error: processing vignette 'tmap-getstarted.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
Packages suggested but not available for checking:
  ‘Rcampdf’ ‘Rpoppler’ ‘tm.lexicon.GeneralInquirer’
Package unavailable to check Rd xrefs: ‘Rpoppler’
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  tmux not found
  1: stop("tmux not found") at testthat/test-server.R:3
  
  ── 3. Error: (unknown) (@test-session.R#3)  ────────────────────────────────────
  tmux not found
  1: stop("tmux not found") at testthat/test-session.R:3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 0 SKIPPED: 0 FAILED: 3
  1. Error: (unknown) (@test-pipe.R#3) 
  2. Error: (unknown) (@test-server.R#3) 
  3. Error: (unknown) (@test-session.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking: ‘RGtk2’ ‘gWidgetsRGtk2’
Package required but not available: ‘qpgraph’

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

Package suggested but not available for checking: ‘rggobi’

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

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

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

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Warning in download.file(url, destfile = tmp, quiet = !messaging, mode = "wb") :
  cannot open URL 'http://maps.googleapis.com/maps/api/staticmap?center=50.824,-1.7133&zoom=13&size=640x640&scale=2&maptype=terrain&sensor=false': HTTP status was '403 Forbidden'
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Error in re-building vignettes:
  ...
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'

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

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



Attaching package: 'adegenet'

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

    AICc

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

    .render.server.info

Quitting from lines 136-138 (DengueVignette.Rmd) 
Error: processing vignette 'DengueVignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is 56.6Mb
  sub-directories of 1Mb or more:
    libs  54.9Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 130-139 (choropleth_maps_with_tricolore.Rmd) 
Error: processing vignette 'choropleth_maps_with_tricolore.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/trinROC.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
Package suggested but not available for checking: ‘TSodbc’
Package unavailable to check Rd xrefs: ‘TSodbc’
Errors in running code in vignettes:
when running code in ‘Guide.Stex’
  ...
> z <- TSget("ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT", 
+     eurostat)
Apr 23, 2018 11:16:19 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
INFO: Contacting web service with query: http://ec.europa.eu/eurostat/SDMX/diss-web/rest/dataflow/ESTAT/ei_nama_q/latest/
Apr 23, 2018 11:16:20 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: (500): Error on the provider side.

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

> options(continue = "  ")

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

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

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

Error: processing vignette 'Guide.Stex' failed with diagnostics:
 chunk 5 
Error in .local(serIDs, con, ...) : 
  ei_nama_q.Q.MIO-EUR.NSA.CP.NA-P72.IT error: it.bancaditalia.oss.sdmx.exceptions.SdmxResponseException: (500): Error on the provider side.
Execution halted
Error in re-building vignettes:
  ...
          separate plot or all together c("single, "multiple)

  Xtitle: A character, set the X axis title, default set to NULL

  Ytitle: A character, set the Y axis title, default set to NULL

   title: A character, set the plot title, default set to NULL

   Xgrid: Logic,show the X axis grid if set to TRUE

   Ygrid: Logic,show the Y axis grid if set to TRUE

_E_x_a_m_p_l_e_s:

     data(USVSales)
     ts_plot(USVSales)
     
     # adding slider
     ts_plot(USVSales, slider = TRUE)
     

Quitting from lines 43-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/TukeyRegion.Rcheck/00install.out’ for details.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc         5.2Mb
    dummydata   1.4Mb
    libs       22.0Mb
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="./webshot6b661ba5942.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file './webshot6b661ba5942.png': No such file or directory
Quitting from lines 59-76 (UKgrid_vignette.Rmd) 
Error: processing vignette 'UKgrid_vignette.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Running ‘testthat.R’ [10s/10s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  test small
  
  test_spectral
  
  test_synthetic
  
  test_universal
  
  test_utils
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 206 SKIPPED: 0 FAILED: 1
  1. Failure: predicted layout is reasonable (@test_naive.R#101) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.6Mb
    libs   2.2Mb
plot.upclassfit: no visible global function definition for ‘frame’
plot.upclassfit: no visible global function definition for ‘par’
plot.upclassfit: no visible global function definition for ‘axis’
plot.upclassfit: no visible global function definition for ‘matplot’
plot.upclassfit: no visible global function definition for ‘legend’
plot.upclassfit: no visible global function definition for ‘title’
Undefined global functions or variables:
  axis frame legend matplot par title
Consider adding
  importFrom("graphics", "axis", "frame", "legend", "matplot", "par",
             "title")
to your NAMESPACE file.
Found the following significant warnings:
  ursa.c:3252:37: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ursa.c:3252:56: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
  ursa.c:3252:75: warning: using integer absolute value function 'abs' when argument is of floating point type [-Wabsolute-value]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ursa.Rcheck/00install.out’ for details.
File ‘uuid/libs/uuid.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘gen_uuid.o’
  Found ‘_srand’, possibly from ‘srand’ (C)
    Object: ‘gen_uuid.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 37.7Mb
  sub-directories of 1Mb or more:
    libs  36.9Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
installed size is 79.0Mb
  sub-directories of 1Mb or more:
    libs  77.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    libs  16.6Mb
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    libs  26.8Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      3.5Mb
    doc    1.2Mb
    help   2.8Mb
Running examples in ‘viridisLite-Ex.R’ failed
The error most likely occurred in:

> ### Name: viridis
> ### Title: Matplotlib 'viridis' and 'cividis' color map
> ### Aliases: viridis viridisMap magma inferno plasma cividis
> 
> ### ** Examples
> 
> library(ggplot2)
Warning: S3 methods ‘.DollarNames.C++Object’, ‘.DollarNames.Module’, ‘print.bytes’, ‘format.Rcpp_stack_trace’, ‘str.Rcpp_stack_trace’, ‘print.Rcpp_stack_trace’ were declared in NAMESPACE but not found
Error: package or namespace load failed for ‘ggplot2’ in library.dynam(lib, package, package.lib):
 shared object ‘Rcpp.so’ not found
Execution halted
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 55.9Mb
  sub-directories of 1Mb or more:
    libs  54.7Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/wand.Rcheck/00install.out’ for details.
Package required but not available: ‘bioacoustics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  1: curl::curl_echo(h) at testthat/test-echo.R:14
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ── 2. Error: Echo a big file (@test-echo.R#51)  ────────────────────────────────
  Callback aborted
  1: curl::curl_echo(h) at testthat/test-echo.R:51
  2: curl_fetch_memory(paste0("http://localhost:", port, "/"), handle = handle)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Error: test echo from httpuv (@test-echo.R#14) 
  2. Error: Echo a big file (@test-echo.R#51) 
  
  Error: testthat unit tests failed
  Execution halted
Malformed Title field: should not end in a period.
Deprecated license: BSD
File ‘webvis/R/zzz.R’:
  .onLoad calls:
    print("Welcome to the webvis pacakge.")

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

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

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

The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Package suggested but not available for checking: ‘org.Mm.eg.db’
Package in Depends field not imported from: ‘snpStats’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Z.value: no visible global function definition for ‘sd’
Z.value: no visible global function definition for ‘pnorm’
pairtest: no visible global function definition for ‘is’
pairtest: no visible global function definition for ‘new’
pairtest: no visible global function definition for ‘rbind2’
pairtest: no visible global function definition for ‘p.value’
pairtest: no visible global function definition for ‘single.snp.tests’
scoretest: no visible global function definition for ‘pchisq’
varplot : <anonymous>: no visible global function definition for ‘var’
varplot: no visible global function definition for ‘plot’
varplot: no visible global function definition for ‘abline’
Undefined global functions or variables:
  abline is new p.value pchisq plot pnorm rbind2 sd single.snp.tests
  var
Consider adding
  importFrom("graphics", "abline", "plot")
  importFrom("methods", "is", "new", "rbind2")
  importFrom("stats", "pchisq", "pnorm", "sd", "var")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Found the following significant warnings:
  t_region.cpp:78:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:115:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  t_info.cpp:120:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/WhopGenome.Rcheck/00install.out’ for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Packages required but not available: ‘gWidgetsRGtk2’ ‘cairoDevice’ ‘RGtk2’

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

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

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

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Error: processing vignette 'modification.Rmd' failed with diagnostics:
shared object 'stringi.so' not found
Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
date	lon	lat	lowLon	higLon	lowLat	higLat
4/23/2003	203.899	19.664	203.899	203.899	19.664	19.664
4/24/2003	204.151	19.821	203.912597	204.389403	18.78051934	20.86148066
4/30/2003	203.919	20.351	203.6793669	204.1586331	18.79728188	21.90471812
5/1/2003	204.229	20.305	203.9943343	204.4636657	18.90440013	21.70559987
Quitting from lines 1055-1057 (Usingxtractomatic.Rmd) 
Error: processing vignette 'Usingxtractomatic.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Found the following significant warnings:
  Warning: package ‘dplyr’ was built under R version 3.5.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/ZipRadius.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.5/zstdr.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    bootstrapping_example   1.1Mb
    libs                    3.5Mb
Error in re-building vignettes:
  ...
Quitting from lines 78-85 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
installed size is 14.4Mb
  sub-directories of 1Mb or more:
    R  14.3Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data       2.7Mb
    pictures   2.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/adnuts.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ANOM.Rcheck/00install.out' for details.
Missing or unexported object: 'rhdf5::h5closeAll'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/aqp.Rcheck/00install.out' for details.
Package suggested but not available for checking: 'AffymetrixDataTestFiles'
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.5Mb
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
'library' or 'require' calls in package code:
  'cacheSweave' 'weaver'
  Please use :: or requireNamespace() instead.
  See section 'Suggested packages' in the 'Writing R Extensions' manual.
Package in Depends field not imported from: 'methods'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
':::' call which should be '::': 'utils:::RtangleSetup'
  See the note in ?`:::` about the use of this operator.
Unexported objects imported by ':::' calls:
  'cacheSweave:::metaChunkName' 'cacheSweave:::metaSetCreationTime'
  'survival:::survmean' 'utils:::.SweaveValidFilenameRegexp'
  'utils:::RtangleFinish' 'utils:::RtangleRuncode'
  'utils:::SweaveParseOptions'
  See the note in ?`:::` about the use of this operator.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(devtools)
  > library(assertive.matrices)
  > 
  > with_envvar(
  +   c(LANG = "en_US"),
  +   test_check("assertive.matrices")
  + )
  Error in with_envvar(c(LANG = "en_US"), test_check("assertive.matrices")) : 
    could not find function "with_envvar"
  Execution halted
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/audio.Rcheck/00install.out' for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
    libs   1.8Mb
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > # Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(badgecreatr)
  > 
  > test_check("badgecreatr")
  -- 1. Error: internetconnection works (@test_badge_placers.R#26)  --------------
  cannot open the connection
  1: expect_equal(readLines("http://www.repostatus.org/#wip")[1], "<!doctype html>") at testthat/test_badge_placers.R:26
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: readLines("http://www.repostatus.org/#wip")
  5: file(con, "r")
  
  -- 2. Error: all status options work (@test_badge_placers.R#30)  ---------------
  cannot open the connection
  1: expect_match(projectstatusbadge("concept"), regexp = "\\[Project Status: Concept") at testthat/test_badge_placers.R:30
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: projectstatusbadge("concept")
  5: readLines(con = projectstatus, encoding = "UTF-8")
  6: file(con, "r")
  
  == testthat results  ===========================================================
  OK: 19 SKIPPED: 3 FAILED: 2
  1. Error: internetconnection works (@test_badge_placers.R#26) 
  2. Error: all status options work (@test_badge_placers.R#30) 
  
  Error: testthat unit tests failed
  Execution halted
Warning in normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="C:\PROGRA~4\Java\JDK18~2.0_1\jre\bin\java.exe": Zugriff verweigert
Warning in normalizePath(path.expand(path), winslash, mustWork) :
  path[1]="C:\PROGRA~4\Java\JDK18~2.0_1\jre": Zugriff verweigert

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.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/bamdit.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BANOVA.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.6Mb
    libs   1.9Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(baseballDBR)
  > 
  > test_check("baseballDBR")
  -- 1. Failure: (unknown) (@test-check_urls.R#25)  ------------------------------
  urlExists("http://www.fangraphs.com/guts.aspx?type=cn") isn't true.
  
  == testthat results  ===========================================================
  OK: 2 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 3 (http://www.fangraphs.com/guts.aspx?type=cn) 
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/bayesCL.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/bayesLopod.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     1.6Mb
    doc   4.0Mb
File 'BayHap/libs/i386/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'
File 'BayHap/libs/x64/BayHap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'mcmc.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'mcmc.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/bea.R.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'methods'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 143.8Mb
  sub-directories of 1Mb or more:
    include  142.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Biocomb.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/bmlm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/BNSP.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/BonEV.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/brainGraph.Rcheck/00install.out' for details.
File 'brainwaver/libs/i386/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'
File 'brainwaver/libs/x64/brainwaver.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'connexity_small_world.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/bssm.Rcheck/00install.out' for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/BVS.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  5.7Mb
  sub-directories of 1Mb or more:
    data     1.5Mb
    models   2.4Mb
Found the following Makefile(s) without a final LF:
  inst/doc/Makefile
Some 'make' programs ignore lines not ending in LF.
Files in the 'vignettes' directory newer than same file in 'inst/doc':
  'figure/glmnet-diagnostic.pdf', 'figure/roc-plot.pdf'
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   2.1Mb
Missing or unexported object: 'utils::askYesNo'
changer: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/cjoint.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/clinDR.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ClusteredMutations.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
    pdf   2.2Mb
Package required but not available: 'BiocManager'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'mogene10sttranscriptcluster.db'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.6Mb
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   6.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/corrgram.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/CPE.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/crossmatch.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/CrossScreening.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/csabounds.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/CsChange.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ctsem.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Daim.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/DatabionicSwarm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/dataMaid.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/DCD.Rcheck/00install.out' for details.
Running 'testthat.R' [75s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(DeclareDesign)
  Loading required package: randomizr
  Loading required package: fabricatr
  Loading required package: estimatr
  > 
  > test_check("DeclareDesign")
  -- 1. Failure: error if you try to draw POs at a level using a variable that doe
  `my_potential_outcomes_formula(pop)` did not throw an error.
  
  == testthat results  ===========================================================
  OK: 436 SKIPPED: 1 FAILED: 1
  1. Failure: error if you try to draw POs at a level using a variable that doesn't exist at that level (@test-potential-outcomes.R#160) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/decomposedPSF.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/demography.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/dendextend.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/DendSer.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    help   1.4Mb
    libs   1.7Mb
Package suggested but not available for checking: 'BiocManager'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/devtools.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

Loading required package: RSQLite
no column `person_id` provided, automatically generating unique person id's
pandoc.exe: Could not fetch img/main_bar.PNG
img/main_bar.PNG: openBinaryFile: does not exist (No such file or directory)
Warning: running command '"D:/compiler/pandoc/pandoc" +RTS -K512m -RTS dextergui.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output dextergui.html --smart --email-obfuscation none --self-contained --standalone --section-divs --table-of-contents --toc-depth 3 --template "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmd\h\default.html" --highlight-style pygments --css "d:\RCompile\CRANpkg\lib\3.4\rmarkdown\rmarkdown\templates\html_vignette\resources\vignette.css" --mathjax --variable "mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML"' had status 67
Error: processing vignette 'dextergui.Rmd' failed with diagnostics:
pandoc document conversion failed with error 67
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/dfped.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/dfpk.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/DGCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/dgo.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/dhglm.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    5.1Mb
    libs   1.4Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    5.6Mb
    libs   1.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/diveRsity.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Dowd.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Running 'testthat.R' [25s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ---
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  -- 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ---
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  == testthat results  ===========================================================
  OK: 2939 SKIPPED: 6 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > 
  > test_check("dplyr")
  -- 1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28)  ---
  `funs(...)` threw an error with unexpected message.
  Expected match: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not `function`"
  Actual message: "`function(si) {\n    mp[si]\n}` must be a function name (quoted or unquoted) or an unquoted call, not ``function``"
  
  -- 2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36)  ---
  `funs(~mp[.])` threw an error with unexpected message.
  Expected match: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not `~`"
  Actual message: "`~mp[.]` must be a function name (quoted or unquoted) or an unquoted call, not ``~``"
  
  == testthat results  ===========================================================
  OK: 2939 SKIPPED: 6 FAILED: 2
  1. Failure: funs() gives a clear error message (#3368) (@test-funs.R#28) 
  2. Failure: funs() gives a clear error message (#3368) (@test-funs.R#36) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a connection 
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.3Mb
    libs   4.3Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    assets        3.4Mb
    htmlwidgets   3.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ecospat.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/edstan.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/eggCounts.Rcheck/00install.out' for details.
Running 'testthat.R' [34s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(egor)
  Loading required package: dplyr
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  Loading required package: tibble
  > library(dplyr)
  > 
  > test_check("egor")
  -- 1. Failure: as_network works. (@test_conversions.R#16)  ---------------------
  include.ego/ego.attrs/ego.alter.weights threw an error.
  Message: replacement has 1 row, data has 0
  Class:   simpleError/error/condition
  
  3 Egos/ Ego Networks 
   31 Alters 
  Average Netsize 10.3333333333333 
  Average Density 0.490616246498599
  Ego sampling design:
    Independent Sampling design (with replacement)
    survey::svydesign(~1, data = egor)
  Alter survey design:
    Maximum nominations: Inf 
  EI-Index: age
  EI-Index: sex
  EI-Index: sex
  EI-Index: int_var
  EI-Index: female
  EI-Index: female
  == testthat results  ===========================================================
  OK: 71 SKIPPED: 0 FAILED: 1
  1. Failure: as_network works. (@test_conversions.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    extdata  10.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    xsd   5.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/enetLTS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EnsCat.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   3.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/EstimateGroupNetwork.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
'getSymbols' currently uses auto.assign=TRUE by default, but will
use auto.assign=FALSE in 0.5-0. You will still be able to use
'loadSymbols' to automatically load data. getOption("getSymbols.env")
and getOption("getSymbols.auto.assign") will still be checked for
alternate defaults.

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


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

This message is shown once per session and may be disabled by setting
options("getSymbols.yahoo.warning"=FALSE).
Warning: ALV.DE contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: CS.PA contains missing values. Some functions will not work if objects contain missing values in the middle of the series. Consider using na.omit(), na.approx(), na.fill(), etc to remove or replace them.
Warning: ELE.PA download failed; trying again.
Quitting from lines 56-64 (estudy2-intro.Rmd) 
Error: processing vignette 'estudy2-intro.Rmd' failed with diagnostics:
ELE.PA download failed after two attempts. Error message:
HTTP error 404.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/EventDetectR.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.8Mb
'LinkingTo' field is unused: package has no 'src' directory
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   1.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/FastRWeb.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/FeaLect.Rcheck/00install.out' for details.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
checkOverlap: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'fieldRS-Ex.R' failed
The error most likely occurred in:

> ### Name: checkOverlap
> ### Title: checkOverlap
> ### Aliases: checkOverlap
> 
> ### ** Examples
> 
> {
+ 
+  require(raster)
+  
+  # build polygons
+  df1 <- data.frame(x=c(1, 5, 10, 2, 1), y=c(10, 9, 8, 7, 10))
+  df2 <- data.frame(x=c(2, 6, 5, 4, 2), y=c(10, 9, 7, 4, 10))
+  p <- list(Polygons(list(Polygon(df1)), ID=1), 
+  Polygons(list(Polygon(df2)), ID=2))
+  p <- SpatialPolygons(p)
+ 
+  # check overlap %
+  checkOverlap(p[1,], p[2,])
+ 
+ }
Loading required package: raster
Loading required package: sp
Error in isFALSE(r1) : could not find function "isFALSE"
Calls: checkOverlap
Execution halted
Error in re-building vignettes:
  ...
Loading required package: sp
Quitting from lines 106-115 (fieldRS.Rmd) 
Error: processing vignette 'fieldRS.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/fitur.Rcheck/00install.out' for details.
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'fivethirtyeight-Ex.R'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ForecastComb.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/fpp2.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    2.1Mb
    libs   1.4Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    data  16.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/gastempt.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs      4.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GeomComb.Rcheck/00install.out' for details.
Running 'testthat.R' [46s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(getTBinR)
  > 
  > test_check("getTBinR")
  -- 1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_b
  plot$labels$fill not equal to `test_label`.
  1/1 mismatches
  x[1]: "`test (test - test)`"
  y[1]: "test (test - test)"
  
  == testthat results  ===========================================================
  OK: 75 SKIPPED: 29 FAILED: 1
  1. Failure: map_tb_burden can have a custom legend specified. (@test-map_tb_burden.R#62) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.7Mb
Package required but not available: 'broom.mixed'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/gimme.Rcheck/00install.out' for details.
Running examples in 'giphyr-Ex.R' failed
The error most likely occurred in:

> ### Name: gif_search
> ### Title: Search GIFs by key words throught giphy API
> ### Aliases: gif_search
> 
> ### ** Examples
> 
> gif_search("cat")
Error in bind_rows_(x, .id) : Argument 19 must be length 1, not 3
Calls: gif_search ... content_exporter -> map_df -> <Anonymous> -> bind_rows_ -> .Call
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Giza.Rcheck/00install.out' for details.
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked'
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Error in re-building vignettes:
  ...
Linked to JAGS 4.2.0
Loaded modules: basemod,bugs

Attaching package: 'R2jags'

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

    traceplot

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

Error: processing vignette 'openbugs.Rnw' failed with diagnostics:
 chunk 12 (label = postprocessKentucky) 
Error : $ operator is invalid for atomic vectors
Execution halted
File 'gnmf/libs/i386/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'
File 'gnmf/libs/x64/gnmf.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'FactorMatrix.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'FactorMatrix.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GOGANPA.Rcheck/00install.out' for details.
Packages listed in more than one of Depends, Imports, Suggests, Enhances:
  'GANPA' 'WGCNA'
A package should be listed in only one of these fields.
'library' or 'require' calls to packages already attached by Depends:
  'GANPA' 'WGCNA'
  Please remove these calls from your code.
Packages in Depends field not imported from:
  'GANPA' 'WGCNA'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
GOGANPA: no visible global function definition for 'GSE.Test.Main'
selectRho: no visible global function definition for
  'scaleFreeFitIndex'
Undefined global functions or variables:
  GSE.Test.Main scaleFreeFitIndex
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.0Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/gppm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/GPRMortality.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    R   6.6Mb
Package suggested but not available for checking: 'taxstats1516'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Greg.Rcheck/00install.out' for details.
Packages required but not available:
  'EnsDb.Hsapiens.v86' 'EnsDb.Mmusculus.v79' 'org.Rn.eg.db'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/greport.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/GroupComparisons.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Loading required package: survival
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "ashg2012.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'ashg2012.tex' failed

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

Type X to quit or <RETURN> to proceed,
or enter new name. (Default extension: sty)
Execution halted
installed size is 131.9Mb
  sub-directories of 1Mb or more:
    java  130.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/hablar.Rcheck/00install.out' for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   9.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/haplo.stats.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hBayesDM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hddtools.Rcheck/00install.out' for details.
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hdnom.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/HH.Rcheck/00install.out' for details.
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    doc          13.7Mb
    htmlwidgets   1.8Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/hIRT.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
Found the following significant warnings:
  Warning: S3 methods 'as.promise.Future', 'as.promise.default', 'as.promise.promise', 'format.promise', 'print.promise' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/htmlwidgets.Rcheck/00install.out' for details.
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    data  12.8Mb
    doc    1.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.8Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   5.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/idem.Rcheck/00install.out' for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  13.8Mb
installed size is 19.7Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       1.1Mb
    include   2.8Mb
    libs     12.9Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    R  10.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/imputeTS.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.labelled', '[.labelled_spss', 'as.data.frame.labelled', 'as_factor.data.frame', 'as_factor.labelled', 'is.na.labelled_spss', 'print.labelled', 'print.labelled_spss', 'type_sum.labelled', 'zap_formats.data.frame', 'zap_formats.default', 'zap_labels.data.frame', 'zap_labels.default', 'zap_labels.labelled', 'zap_labels.labelled_spss', 'zap_missing.data.frame', 'zap_missing.default', 'zap_missing.labelled', 'zap_missing.labelled_spss', 'zap_widths.data.frame', 'zap_widths.default' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.4/intsvy.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data      1.3Mb
    extdata   7.5Mb
Running 'testthat.R' [73s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ipeaData)
  > 
  > test_check("ipeaData")
  [1] "NA. 05/1999 a 03/2009. Acesso em: 25/10/2018"
  -- 1. Error: ipeaData (@test_functions_ipea_data.R#19)  ------------------------
  Recv failure: Connection was reset
  1: suppressWarnings(result <- ipeadata("SERIE SEM RETORNO")) at testthat/test_functions_ipea_data.R:19
  2: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  3: ipeadata("SERIE SEM RETORNO")
  4: get_metadata(serie)
  5: basic_call(api_call, type)
  6: GET(api)
  7: request_perform(req, hu$handle$handle)
  8: request_fetch(req$output, req$url, handle)
  9: request_fetch.write_memory(req$output, req$url, handle)
  10: curl::curl_fetch_memory(url, handle = handle)
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 1
  1. Error: ipeaData (@test_functions_ipea_data.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/IsingFit.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/LexisNexisTools.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      3.4Mb
unshelf: no visible global function definition for '...length'
Undefined global functions or variables:
  ...length
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/lifecourse.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   3.0Mb
AQSys.plot: no visible binding for global variable 'x'
AQSys.plot: no visible binding for global variable 'y'
Undefined global functions or variables:
  x y
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    libs       2.1Mb
    testdata   1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/LogisticDx.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/lordif.Rcheck/00install.out' for details.
installed size is 41.2Mb
  sub-directories of 1Mb or more:
    doc    6.8Mb
    libs  34.2Mb
is_literally_false: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.4Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   1.6Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Mcomp.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.6Mb
    libs      1.5Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.0Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    doc    1.0Mb
    libs   3.9Mb
    misc   1.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/mgm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/microplot.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/MiRAnorm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/MissingDataGUI.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   4.9Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  20.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/molaR.Rcheck/00install.out' for details.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    1.7Mb
    libs   1.9Mb
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    libs  12.6Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/MortalityGaps.Rcheck/00install.out' for details.
Running examples in 'MoTBFs-Ex.R' failed
The error most likely occurred in:

> ### Name: MoTBFs_Learning
> ### Title: Learning MoTBFs in a Network
> ### Aliases: MoTBFs_Learning
> 
> ### ** Examples
> 
> ## Dataset Ecoli
> require(MoTBFs)
> data(ecoli)
> data <- ecoli[,-c(1)] ## remove variable sequence
> 
> ## Directed acyclic graph
> dag <- LearningHC(data)
> 
> ## Learning BN
> intervals <- 3
> potential <- "MOP"
> P1 <- MoTBFs_Learning(graph = dag, data = data, POTENTIAL_TYPE=potential,
+ maxParam = 5)
Error in lapply(X = X, FUN = FUN, ...) : 
  argument "numIntervals" is missing, with no default
Calls: MoTBFs_Learning ... learn.tree.Intervals -> quantileIntervals -> sapply -> lapply
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/mrMLM.GUI.Rcheck/00install.out' for details.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    libs  19.8Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
Error in re-building vignettes:
  ...
Quitting from lines 43-50 (mstrio.Rmd) 
Error: processing vignette 'mstrio.Rmd' failed with diagnostics:
Authentication error. Check user credentials or REST API URL and try again.
HTTP 401 Unauthorized, Client error: (401) Unauthorized
I-Server Error ERR003, Login failed
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/multilevelPSA.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'stringi'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/MXM.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.4Mb
    libs   1.5Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.0Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/NetworkComparisonTest.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/newsmap.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.5Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.9Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/nonparaeff.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Warning: running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "nonrandom.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.4.4/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.4.4/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'nonrandom.tex' failed

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

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

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

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R            1.4Mb
    test_files   4.2Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    help   2.4Mb
    libs   2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    nifti   3.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc   5.9Mb
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(osrmr)
  > 
  > test_check("osrmr")
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  Error in file(con, "r") : cannot open the connection
  -- 1. Error: viaroute finds routes (@test-basic_functions.R#15)  ---------------
  $ operator is invalid for atomic vectors
  1: expect_equal(viaroute(lat1, lng1, lat2, lng2, F, api_version, localhost), 1560, tolerance = 300, 
         scale = 1) at testthat/test-basic_functions.R:15
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: viaroute(lat1, lng1, lat2, lng2, F, api_version, localhost)
  5: viaroute_api_v5(lat1, lng1, lat2, lng2, instructions, address)
  6: assertthat::assert_that(assertthat::is.number(res$routes[[1]]$duration))
  7: see_if(..., env = env, msg = msg)
  8: tryCatch({
         eval(assertion, env)
     }, assertError = function(e) {
         structure(FALSE, msg = e$message)
     })
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: doTryCatch(return(expr), name, parentenv, handler)
  12: eval(assertion, env)
  13: eval(assertion, env)
  14: assertthat::is.number(res$routes[[1]]$duration)
  
  == testthat results  ===========================================================
  OK: 13 SKIPPED: 1 FAILED: 1
  1. Error: viaroute finds routes (@test-basic_functions.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [7s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("pacman")
  > options(repos="http://cran.rstudio.com/")
  > 
  > 
  > test_check("pacman")
  -- 1. Error: p_install_gh works (@test-p_install_gh.R#5)  ----------------------
  HTTP error 404.
    Not Found
  
    Rate limit remaining: 59/60
    Rate limit reset at: 2018-10-22 00:51:57 UTC
  
    
  1: expect_false(p_install_gh("greg/iDontExistAnywhere")) at testthat/test-p_install_gh.R:5
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: p_install_gh("greg/iDontExistAnywhere")
  5: lapply(package, function(x) {
         devtools::install_github(x, dependencies = dependencies, ...)
     })
  6: FUN(X[[i]], ...)
  7: devtools::install_github(x, dependencies = dependencies, ...)
  8: install_remotes(remotes, auth_token = auth_token, host = host, dependencies = dependencies, 
         upgrade = upgrade, force = force, quiet = quiet, build = build, build_opts = build_opts, 
         repos = repos, type = type, ...)
  9: vapply(remotes, install_remote, ..., FUN.VALUE = character(1))
  10: FUN(X[[i]], ...)
  11: remote_package_name(remote)
  12: remote_package_name.github_remote(remote)
  13: github_DESCRIPTION(username = remote$username, repo = remote$repo, subdir = remote$subdir, 
         host = remote$host, ref = remote$ref, pat = remote$auth_token %||% github_pat(), 
         use_curl = use_curl)
  
  == testthat results  ===========================================================
  OK: 54 SKIPPED: 3 FAILED: 1
  1. Error: p_install_gh works (@test-p_install_gh.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...


Error: processing vignette 'PANDA.Rnw' failed with diagnostics:
 chunk 6 
Error in initialize(value, ...) : 
  argument "go_id" is missing, with no default
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/papayar.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'BBmisc::isFALSE' by 'backports::isFALSE' when loading 'ParamHelpers'
See 'd:/Rcompile/CRANpkg/local/3.4/ParamHelpers.Rcheck/00install.out' for details.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > std_getwd <- function() 
  + {
  +   pwd <- getwd()
  +   # Enforce upper case Windows drive letters
  +   substring(pwd, 1, 1) <- toupper(substring(pwd, 1, 1))
  +   pwd
  + }
  > 
  > test_check("pathological")
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.4/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    lib    5.8Mb
    libs   4.8Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    1.1Mb
    libs   1.4Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   2.7Mb
    libs      1.8Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/peRiodiCS.Rcheck/00install.out' for details.
Running examples in 'phyloseqGraphTest-Ex.R' failed
The error most likely occurred in:

> ### Name: graph_perm_test
> ### Title: Performs graph-based permutation tests
> ### Aliases: graph_perm_test
> 
> ### ** Examples
> 
> library(phyloseq)
> data(enterotype)
> gt = graph_perm_test(enterotype, sampletype = "SeqTech", type = "mst")
Error in .C("veg_distance", x = as.double(x), nr = N, nc = ncol(x), d = double(N *  : 
  "veg_distance" not available for .C() for package "vegan"
Calls: graph_perm_test ... distance -> do.call -> do.call -> vegdist -> vegdist -> .C
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 128-134 (gt_vignette.Rmd) 
Error: processing vignette 'gt_vignette.Rmd' failed with diagnostics:
"veg_distance" not available for .C() for package "vegan"
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/pingers.Rcheck/00install.out' for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.9Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.3Mb
    libs   1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/pompom.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
File 'powell/libs/i386/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'
File 'powell/libs/x64/powell.dll':
  Found 'printf', possibly from 'printf' (C)
    Object: 'powell.o'
  Found 'puts', possibly from 'printf' (C), 'puts' (C)
    Object: 'powell.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/preText.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.6Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    extdata   6.4Mb
    libs      1.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/ProjectionBasedClustering.Rcheck/00install.out' for details.
Missing or unexported objects:
  'brms::data_response' 'brms::update_adterms'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/prophet.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/PST.Rcheck/00install.out' for details.
simulate_data_regression: possible error in diag(x = 1, nrow = n_var +
  1, ncol = n_var + 1, names = TRUE): unused argument (names = TRUE)
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'psycho-Ex.R'
Running examples in 'psycho-Ex.R' failed
The error most likely occurred in:

> ### Name: simulate_data_regression
> ### Title: Simulates data for single or multiple regression.
> ### Aliases: simulate_data_regression
> 
> ### ** Examples
> 
> library(psycho)
> 
> data <- simulate_data_regression(coefs=c(0.1, 0.8), sample=50, error=0)
Error in diag(x = 1, nrow = n_var + 1, ncol = n_var + 1, names = TRUE) : 
  unused argument (names = TRUE)
Calls: simulate_data_regression
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc        4.6Mb
    examples   2.2Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/qgraph.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Quitting from lines 112-113 (orthography_processing.Rmd) 
Error: processing vignette 'orthography_processing.Rmd' failed with diagnostics:
undefined columns selected
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   3.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   2.1Mb
File 'QUIC/libs/i386/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'
File 'QUIC/libs/x64/QUIC.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'QUIC.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'QUIC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Package suggested but not available for checking: 'rcom'
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    3.7Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   8.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RAM.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs   2.8Mb
Error in re-building vignettes:
  ...
Loading required package: sp
Loading required package: RANN
Loading required package: PBSmapping

-----------------------------------------------------------
PBS Mapping 2.70.5 -- Copyright (C) 2003-2018 Fisheries and Oceans Canada

PBS Mapping comes with ABSOLUTELY NO WARRANTY;
for details see the file COPYING.
This is free software, and you are welcome to redistribute
it under certain conditions, as outlined in the above file.

A complete user guide 'PBSmapping-UG.pdf' is located at 
d:/RCompile/CRANpkg/lib/3.4/PBSmapping/doc/PBSmapping-UG.pdf

Packaged on 2018-06-05
Pacific Biological Station, Nanaimo

All available PBS packages can be found at
https://github.com/pbs-software

To see demos, type '.PBSfigs()'.
-----------------------------------------------------------


Warning in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) :
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true': HTTP status was '403 Forbidden'

Error: processing vignette 'RapidPolygonLookup.Rnw' failed with diagnostics:
 chunk 1 
Error in download.file(urlStr, destfile, mode = "wb", quiet = TRUE) : 
  cannot open URL 'http://maps.google.com/maps/api/staticmap?center=37.77173,-122.4306&zoom=13&size=550x550&maptype=mobile&format=png32&sensor=true'
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.3Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    etc    1.9Mb
    po     1.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.7Mb
Error in re-building vignettes:
  ...
Loading required package: sp

Attaching package: 'dplyr'

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

    intersect, select, union

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

    filter, lag

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

    intersect, setdiff, setequal, union

rgdal: version: 1.3-6, (SVN revision 773)
 Geospatial Data Abstraction Library extensions to R successfully loaded
 Loaded GDAL runtime: GDAL 2.2.3, released 2017/11/20
 Path to GDAL shared files: d:/RCompile/CRANpkg/lib/3.4/rgdal/gdal
 GDAL binary built with GEOS: TRUE 
 Loaded PROJ.4 runtime: Rel. 4.9.3, 15 August 2016, [PJ_VERSION: 493]
 Path to PROJ.4 shared files: d:/RCompile/CRANpkg/lib/3.4/rgdal/proj
 Linking to sp version: 1.3-1
indexplot: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'RcmdrMisc-Ex.R' failed
The error most likely occurred in:

> ### Name: indexplot
> ### Title: Index Plots
> ### Aliases: indexplot
> ### Keywords: hplot
> 
> ### ** Examples
> 
> if (require("car")){
+     with(Prestige, indexplot(income, id.n=2, labels=rownames(Prestige)))
+     indexplot(Prestige[, c("income", "education", "prestige")], 
+         groups = Prestige$type, id.n=2)
+ }
Error in isFALSE(legend) : could not find function "isFALSE"
Calls: with -> with.default -> eval -> eval -> indexplot
Execution halted
Package required and available but unsuitable version: 'effects'

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

> ### Name: fetch_deputado
> ### Title: Retrieves details about a deputy
> ### Aliases: fetch_deputado
> 
> ### ** Examples
> 
> abel_mesquita_info <- fetch_deputado(id = 178957)
Error: API did not return json
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    include   6.3Mb
    libs      2.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Running 'testthat.R' [38s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("rdefra")
  > 
  > test_check("rdefra")
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  Error in file(file, "rt") : cannot open the connection
  -- 1. Failure: Metadata should be in the right format (@test-data.R#44)  -------
  `x` not equal to `expected`.
  1 element mismatch
  
  Error in file(file, "rt") : cannot open the connection
  -- 2. Failure: Data should be in the right format (@test-data.R#55)  -----------
  `x` not equal to `expected`.
  'is.NA' value mismatch: 0 in current 1 in target
  
  == testthat results  ===========================================================
  OK: 39 SKIPPED: 1 FAILED: 2
  1. Failure: Metadata should be in the right format (@test-data.R#44) 
  2. Failure: Data should be in the right format (@test-data.R#55) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'RedditExtractoR-Ex.R' failed
The error most likely occurred in:

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

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

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

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

  |                                                                            
  |======================================================================| 100%
> network_list <- target_df %>% user_network(include_author=FALSE, agg=TRUE) # extract the network
Error in left_join_impl(x, y, by_x, by_y, aux_x, aux_y, na_matches) : 
  Can't join on 'response_to' x 'response_to' because of incompatible types (factor / logical)
Calls: %>% ... left_join -> left_join.tbl_df -> left_join_impl -> .Call
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
rec: no visible global function definition for 'isFALSE'
reweight.contingencytable: no visible global function definition for
  'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'revengc-Ex.R' failed
The error most likely occurred in:

> ### Name: rec
> ### Title: Reverse engineering censored and decoupled data
> ### Aliases: rec
> ### Keywords: Poisson negative binomial univariate table frequency table
> ###   count data censored dispersion truncated contingency
> 
> ### ** Examples
> 
>   # provide two averages
>   # seed.matrix defaults to a matrix of ones
>   # seed.estimation.method defaults to ipfp
>   twoaverages.results<-rec(
+      X= 4.4,
+      Y = 571.3,
+      Xlowerbound = 1,
+      Xupperbound = 20,
+      Ylowerbound = 520,
+      Yupperbound = 620)
[1] "Truncated Poisson distributions were calculated for both the X and Y variable (i.e. Var(X) = E(X) and Var(Y) = E(Y) has to be assumed when only averages are provided)"
[1] "The default seed matrix implies independence between variables 1/(length(Xlowerbound:Xupperbound)*length(Ylowerbound:Yupperbound)) (i.e. independence between variables has to be assumed when there is no external information about the joint distribution)"
Error in isFALSE(all.equal(sum(seedfinal), 1)) : 
  could not find function "isFALSE"
Calls: rec
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/Rfast.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/RFmarkerDetector.Rcheck/00install.out' for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is 80.0Mb
  sub-directories of 1Mb or more:
    gdal       3.9Mb
    libs      68.7Mb
    pictures   1.3Mb
    proj       5.0Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    doc     3.9Mb
    fonts   1.5Mb
    libs    2.0Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    extra   9.3Mb
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   5.1Mb
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.4/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    rmd   6.7Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/rms.Rcheck/00install.out' for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      5.5Mb
Packages required and available but unsuitable versions:
  'impute' 'MassSpecWavelet'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Packages suggested but not available for checking:
  'hgu95av2cdf' 'illuminaHumanv3.db'
summarizeNumerics: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'rockchalk-Ex.R' failed
The error most likely occurred in:

> ### Name: addLines
> ### Title: Superimpose regression lines on a plotted plane
> ### Aliases: addLines
> 
> ### ** Examples
> 
> ##library(rockchalk)
> 
> 
> set.seed(12345)
> 
> dfadd <- genCorrelatedData2(100, means = c(0,0,0,0), sds = 1, rho = 0,
+        beta = c(0.03, 0.01, 0.1, 0.4, -0.1), stde = 2)
[1] "The equation that was calculated was"
y = 0.03 + 0.01*x1 + 0.1*x2 + 0.4*x3 + -0.1*x4 
 + 0*x1*x1 + 0*x2*x1 + 0*x3*x1 + 0*x4*x1 
 + 0*x1*x2 + 0*x2*x2 + 0*x3*x2 + 0*x4*x2 
 + 0*x1*x3 + 0*x2*x3 + 0*x3*x3 + 0*x4*x3 
 + 0*x1*x4 + 0*x2*x4 + 0*x3*x4 + 0*x4*x4 
 + N(0,2) random error 
> 
> dfadd$xcat1 <- gl(2,50, labels=c("M","F"))
> 
> dfadd$xcat2 <- cut(rnorm(100), breaks=c(-Inf, 0, 0.4, 0.9, 1, Inf),
+                    labels=c("R", "M", "D", "P", "G"))
> 
> dfadd$y2 <- 0.03 + 0.1*dfadd$x1 + 0.1*dfadd$x2 +
+     0.25*dfadd$x1*dfadd$x2 + 0.4*dfadd$x3 - 0.1*dfadd$x4 +
+     0.2 * as.numeric(dfadd$xcat1) +
+     contrasts(dfadd$xcat2)[as.numeric(dfadd$xcat2), ] %*% c(-0.1, 0.1, 0.2, 0) +
+     1 * rnorm(100)
> 
> summarize(dfadd)
Error in isFALSE(probs) : could not find function "isFALSE"
Calls: summarize -> do.call -> summarizeNumerics
Execution halted
Error in re-building vignettes:
  ...
Loading required package: carData

Error: processing vignette 'rockchalk.Rnw' failed with diagnostics:
 chunk 4 
Error in isFALSE(probs) : could not find function "isFALSE"
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R         2.7Mb
    extdata   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.8Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.7Mb
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.4Mb
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.4/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.4/Rserve/libs/i386/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'd:/Rcompile/CRANpkg/lib/3.4/Rserve/libs/x64/Rserve.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
  Found 'exit', possibly from 'exit' (C), 'stop' (Fortran)
  Found 'rand', possibly from 'rand' (C)
  Found 'srand', possibly from 'srand' (C)
File 'Rserve/libs/i386/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'
File 'Rserve/libs/x64/Rserve.dll':
  Found non-API calls to R: 'R_Interactive', 'Rf_initialize_R',
    'setup_Rmainloop'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    doc    3.4Mb
    libs  17.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/rstan.Rcheck/00install.out' for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   5.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   1.8Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.2Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   3.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   2.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/semPlot.Rcheck/00install.out' for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.4Mb
    sequences   1.9Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/seriation.Rcheck/00install.out' for details.
installed size is 95.0Mb
  sub-directories of 1Mb or more:
    doc     11.8Mb
    gdal     3.9Mb
    libs    70.0Mb
    proj     5.0Mb
    sqlite   1.5Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/sharpshootR.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   7.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    www   6.3Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/shrink.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc   6.5Mb
Package suggested but not available for checking: 'BSgenome.Hsapiens.UCSC.hg38'
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/SimRepeat.Rcheck/00install.out' for details.
ExpCatViz: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'SmartEDA-Ex.R' failed
The error most likely occurred in:

> ### Name: ExpCatViz
> ### Title: Distributions of categorical variables
> ### Aliases: ExpCatViz
> 
> ### ** Examples
> 
> ExpCatViz(data=mtcars,gp=NULL,fname=file.path(tempdir(),"Cat_1"),clim=10,margin=1,Page = c(2,2))
Error in isFALSE(rdata) : could not find function "isFALSE"
Calls: ExpCatViz
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-164 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
could not find function "isFALSE"
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/snipEM.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/SNPassoc.Rcheck/00install.out' for details.
Running examples in 'SocialMediaMineR-Ex.R' failed
The error most likely occurred in:

> ### Name: get_reddit
> ### Title: Retrieves detailed information about URLs on Reddit
> ### Aliases: get_reddit
> ### Keywords: OI utilits
> 
> ### ** Examples
> 
> get_reddit("http://i.imgur.com/rSnA8.png")
Error : lexical error: invalid char in json text.
                                       <!doctype html><html><title>Ow!
                     (right here) ------^

Error in temp$data : $ operator is invalid for atomic vectors
Calls: get_reddit -> data.frame
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/soilDB.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.2Mb
sgmix: no visible global function definition for 'isFALSE'
Undefined global functions or variables:
  isFALSE
Running examples in 'spagmix-Ex.R' failed
The error most likely occurred in:

> ### Name: lgcpmix
> ### Title: Generate a spatial log-Gaussian Cox process intensity
> ### Aliases: lgcpmix
> 
> ### ** Examples
> 
> ## Homogeneous example ##
> 
> # Create constant intensity image integrating to 500
> 
> homog <- as.im(as.mask(toywin))
> homog <- homog/integral(homog)*500
> 
> 
> # Corresponding LGCP realisations using exponential covariance structure
> par(mfrow=c(2,2),mar=rep(1.5,4))
> for(i in 1:4){
+   temp <- lgcpmix(homog,covmod="exp",covpars=list(var=1,scale=0.2))
+   plot(temp,main=paste("Realisation",i),log=TRUE)
+ }
> 
> 
> 
> ## Inhomogeneous examples ##
> 
> # Create deterministic trend
> 
> mn <- cbind(c(0.25,0.8),c(0.31,0.82),c(0.43,0.64),c(0.63,0.62),c(0.21,0.26))
> v1 <- matrix(c(0.0023,-0.0009,-0.0009,0.002),2)
> v2 <- matrix(c(0.0016,0.0015,0.0015,0.004),2)
> v3 <- matrix(c(0.0007,0.0004,0.0004,0.0011),2)
> v4 <- matrix(c(0.0023,-0.0041,-0.0041,0.0099),2)
> v5 <- matrix(c(0.0013,0.0011,0.0011,0.0014),2)
> vr <- array(NA,dim=c(2,2,5))
> for(i in 1:5) vr[,,i] <- get(paste("v",i,sep=""))
> intens <- sgmix(mean=mn,vcv=vr,window=toywin,p0=0.1,int=500)
Error in isFALSE(all.equal(sum(c(0.3, p)), 1)) : 
  could not find function "isFALSE"
Calls: sgmix
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/sparseLTSEigen.Rcheck/00install.out' for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.4Mb
Found the following significant warnings:
  Warning: 'devtools::use_package' is deprecated.
See 'd:/Rcompile/CRANpkg/local/3.4/spectrolab.Rcheck/00install.out' for details.
Running examples in 'spm12r-Ex.R' failed
The error most likely occurred in:

> ### Name: install_spm12
> ### Title: Install SPM12 file into directory
> ### Aliases: install_spm12
> 
> ### ** Examples
> 
> tdir = tempfile()
> dir.create(tdir)
> res = install_spm12(install_dir = tdir)
cloning into 'D:\temp\Rtmpue11cF\fileecb81c8f92b/spm12'...
Error in git2r::clone("https://github.com/muschellij2/spm12r", branch = "gh-pages",  : 
  Error in 'git2r_clone': unknown certificate check failure
Calls: install_spm12 -> <Anonymous> -> .Call
Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.7Mb
Warning in parse(file = files, n = -1L) :
  invalid input found on input connection 'stability-Ex.R'
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    include   9.3Mb
Error in re-building vignettes:
  ...
Quitting from lines 47-52 (staple_example.Rmd) 
Error: processing vignette 'staple_example.Rmd' failed with diagnostics:
incorrect number of dimensions
Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   4.9Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    doc   6.4Mb
    nc    2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R          1.9Mb
    datasets   2.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/stpp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/stringi.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/stR.Rcheck/00install.out' for details.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   1.0Mb
    libs   1.7Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/svars.Rcheck/00install.out' for details.
File 'svmpath/libs/i386/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'
File 'svmpath/libs/x64/svmpath.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'mi02lib.o', 'mi05funs.o', 'mi10unix.o', 'mi11sys.o',
      'mi12solv.o', 'mi20amat.o', 'mi25bfac.o', 'mi26bfac.o',
      'mi27lu.o', 'mi30spec.o', 'mi35mps.o', 'mi36mps.o', 'mi40bfil.o',
      'mi50lp.o', 'mi60srch.o', 'mi65rmod.o', 'mi70nobj.o',
      'mi80ncon.o', 'mi81ncon.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/Tcomp.Rcheck/00install.out' for details.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    sql   8.6Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   2.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/testforDEP.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   1.5Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.1Mb
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
File 'tpr/libs/i386/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'
File 'tpr/libs/x64/tpr.dll':
  Found '_ZSt4cerr', possibly from 'std::cerr' (C++)
    Object: 'utils.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data      2.1Mb
    doc       2.5Mb
    extdata   8.4Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/TraMineRextras.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'tram.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tree.bins.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_
Execution halted
Error in re-building vignettes:
  ...

Error: processing vignette 'treecm.Rnw' failed with diagnostics:
 chunk 18 (label = allometryEx1) 
Error : package or namespace load failed for 'reshape2' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_
Execution halted
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
See section 'Generic functions and methods' in the 'Writing R
Extensions' manual.
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
The argument of a replacement function which corresponds to the right
hand side must be named 'value'.
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
See chapter 'System and foreign language interfaces' in the 'Writing R
Extensions' manual.
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: <Anonymous>
Execution halted
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
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 'treeDA-Ex.R' failed
The error occurred in:


R version 3.4.4 (2018-03-15) -- "Someone to Lean On"
Copyright (C) 2018 The R Foundation for Statistical Computing
Platform: x86_64-w64-mingw32/x64 (64-bit)

R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.

  Natural language support but running in an English locale

R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.

Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.

> pkgname <- "treeDA"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('treeDA')
Error: package or namespace load failed for 'treeDA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'treeda-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Running examples in 'treedater-Ex.R' failed
The error most likely occurred in:

> ### Name: sampleYearsFromLabels
> ### Title: Compute a vector of numeric sample times from labels in a
> ###   sequence aligment or phylogeny
> ### Aliases: sampleYearsFromLabels
> 
> ### ** Examples
> 
> ## A couple of labels for Ebola virus sequences: 
> sampleYearsFromLabels( c('EBOV|AA000000|EM104|SierraLeone_EM|2014-06-02'
+                        , 'EBOV|AA000000|G3713|SierraLeone_G|2014-06-09')
+ , delimiter='|' )
Error in sampleYearsFromLabels(c("EBOV|AA000000|EM104|SierraLeone_EM|2014-06-02",  : 
   The `sampleYearsFromLabels` function requires the `lubridate` package. Please install `lubridate`. Stopping.
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'h3n2.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Running examples in 'treeman-Ex.R' failed
The error most likely occurred in:

> ### Name: searchTxnyms
> ### Title: Get node labels based on online taxonomic database
> ### Aliases: searchTxnyms
> 
> ### ** Examples
> 
> tree <- randTree(8)
> new_tids <- c("Gallus_gallus", "Aileuropoda_melanoleucha", "Ailurus_fulgens",
+ "Rattus_rattus", "Mus_musculus", "Gorilla_gorilla", "Pan_trogoldytes", "Homo_sapiens")
> tree <- setNdsID(tree, tree['tips'], new_tids)
> nd_labels <- searchTxnyms(tree)
Error in library.dynam(lib, package, package.lib) : 
  DLL 'stringi' not found: maybe not installed for this architecture?
Calls: searchTxnyms ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Running examples in 'treeman-Ex.R' failed
The error most likely occurred in:

> ### Name: searchTxnyms
> ### Title: Get node labels based on online taxonomic database
> ### Aliases: searchTxnyms
> 
> ### ** Examples
> 
> tree <- randTree(8)
> new_tids <- c("Gallus_gallus", "Aileuropoda_melanoleucha", "Ailurus_fulgens",
+ "Rattus_rattus", "Mus_musculus", "Gorilla_gorilla", "Pan_trogoldytes", "Homo_sapiens")
> tree <- setNdsID(tree, tree['tips'], new_tids)
> nd_labels <- searchTxnyms(tree)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: searchTxnyms ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction-to-treemapify.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'treemap-color_mapping.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_d
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    4.7Mb
    libs   1.5Mb
Loading this package had a fatal error status code 1
Loading log:
Loading required package: ape
Loading required package: ade4
Creating a generic function for 'toJSON' from package 'jsonlite' in package 'googleVis'
Error: package or namespace load failed for 'treespace' in library.dynam(lib, package, package.lib):
 DLL 'stringi' not found: maybe not installed for this architecture?
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'R_API_for_Trello.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'tribe-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'tricolore' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'r_radix.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'trimr-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'trip.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'read-gtfs-files.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'trustOptim-demo.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tryCatchLog-intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'convert.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/tsBSS.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, str
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'tsensembler' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
Running examples in 'tsfknn-Ex.R' failed
The error most likely occurred in:

> ### Name: autoplot.knnForecast
> ### Title: Create a ggplot object from a knnForecast object
> ### Aliases: autoplot.knnForecast
> 
> ### ** Examples
> 
> pred <- knn_forecasting(USAccDeaths, h = 12, lags = 1:12, k = 2)
> library(ggplot2)
> autoplot(pred)
> autoplot(pred, highlight = "neighbors")
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: <Anonymous> ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tsfknn.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'tsiR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: ggplot2
Loading required package: TSP
Loading required package: MASS
Error: package or namespace load failed for 'tspmeta' in library.dynam(lib, package, package.lib):
 DLL 'stringi' not found: maybe not installed for this architecture?
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'tstools.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'basic_tubern.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tuber-ex.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'example.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'ExamplesTukeytrendtest.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'turner_introduction.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_det
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tutorial-basics.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'tvm' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'tvReg-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'tweet2r' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'twfy.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'twilio' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.4/uaparserjs.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'gdalUtils::gdal_rasterize' by 'sf::gdal_rasterize' when loading 'uavRmp'
See 'd:/Rcompile/CRANpkg/local/3.4/uavRmp.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'uavRmp' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ubci' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ubeR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ucbthesis' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'udpipe-annotation.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'intro-to-uGMAR.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'pkg-templates.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ukbtools' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'umap.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: OpenMx
Error: package or namespace load failed for 'umx' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Complete_examples.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'ungroup' in library.dynam(lib, package, package.lib):
 DLL 'stringi' not found: maybe not installed for this architecture?
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'unifDAG-vignette.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'unitedR.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'u0_unitizer_index.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'measurement_units_in_R.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'overview.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'unvotes.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'updog' in library.dynam(lib, package, package.lib):
 DLL 'stringi' not found: maybe not installed for this architecture?
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'upm-primer.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri
Execution halted
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc   7.9Mb
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'uptasticsearch' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'upwaver.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'urlshorteneR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_an
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'urltools.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'userfriendlyscience' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplic
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Data_sources_and_cleaning.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'usl.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_de
Execution halted
Running examples in 'usmap-Ex.R' failed
The error most likely occurred in:

> ### Name: map_with_data
> ### Title: Join county or state level data to US map data
> ### Aliases: map_with_data
> 
> ### ** Examples
> 
> state_data <- data.frame(fips = c("01", "02", "04"), values = c(1, 5, 8))
> df <- map_with_data(state_data, na = 0)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: map_with_data ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'utf8.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'utilsIPEA' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, 
Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(utiml)
  Loading required package: mldr
  Loading required package: parallel
  > 
  > test_check("utiml")
  -- 1. Error: test train/prediction base learner algorithms (@test_base_learner.R
  There are no installed package 'C50' to use C5.0 classifier as base method
  1: mltrain(testdataset) at testthat/test_base_learner.R:20
  2: mltrain.baseC5.0(testdataset)
  3: stop(paste("There are no installed package 'C50' to use C5.0 classifier", "as base method"))
  
  == testthat results  ===========================================================
  OK: 1127 SKIPPED: 21 FAILED: 1
  1. Error: test train/prediction base learner algorithms (@test_base_learner.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'utiml-overview.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
File 'uuid/libs/i386/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'
File 'uuid/libs/x64/uuid.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'gen_uuid.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'gen_uuid.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Error in re-building vignettes:
  ...
Error: processing vignette 'regress_intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(valaddin)
  > 
  > test_check("valaddin")
  Error: package or namespace load failed for 'stringr' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'valaddin.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'validatejsonr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'indicators.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, st
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'vamc' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'vanddraabe' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vapour.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'varband-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'cd.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_det
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/varian.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
Error: processing vignette 'varrank.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Running examples in 'vcfR-Ex.R' failed
The error most likely occurred in:

> ### Name: Format conversion
> ### Title: Convert vcfR objects to other formats
> ### Aliases: 'Format conversion' vcfR2genind vcfR2loci vcfR2genlight
> 
> ### ** Examples
> 
> data(vcfR_test)
> gl <- vcfR2genlight(vcfR_test)
Warning in vcfR2genlight(vcfR_test) :
  Found 2 loci with more than two alleles.
Objects of class genlight only support loci with two alleles.
2 loci will be omitted from the genlight object.
Loading required namespace: adegenet
Failed with error:  'ICU init failed: U_FILE_ACCESS_ERROR'
Warning in vcfR2genlight(vcfR_test) : adegenet not installed
Error in inDL(x, as.logical(local), as.logical(now), ...) : 
  ICU init failed: U_FILE_ACCESS_ERROR
Calls: vcfR2genlight ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'converting_data.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'configuration.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vdg.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_de
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'intro_to_vegalite.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Error in re-building vignettes:
  ...
Loading required package: Rcpp
Loading required package: permute
Loading required package: lattice
This is vegan 2.5-2
Error: processing vignette 'CTA.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_de
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'helpers.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_en
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'using_the_vennLasso_package.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: sp
Error: package or namespace load failed for 'vetools' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'alike.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.2Mb
    help   2.7Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'introduction_to_vimp.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_de
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'abalone-example.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'using_virustotal.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc           5.6Mb
    htmlwidgets   3.9Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'Introduction-to-visNetwork.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'quick-start.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, str
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/visvow.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'visvow' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, str
Execution halted
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/VizOR.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'vmd' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vortexRguide.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, st
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'vosonSML' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'intro_to_voteogram.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_dete
Execution halted
Running 'test-add_sim_index_number.R' [4s]
  Running 'test-filter_dv.R' [0s]
  Running 'test-labeller.R' [6s]
  Running 'test-softwaretype.R' [1s]
  Running 'test-strat-col-detection.R' [0s]
  Running 'test-vpc.R' [7s]
  Running 'test-vpc_cat.R' [3s]
Running the tests in 'tests/test-vpc_cat.R' failed.
Complete output:
  > library(vpc)
  > library(testit)
  > Sys.setenv("R_TESTS" = "")
  > 
  > tmp <- simple_data
  > cat <- cut(tmp$obs$DV, breaks = c(-1, 10, 40, 1000))
  > tmp$obs$DV <- match(cat, levels(cat))
  > cat2 <- cut(tmp$sim$DV, breaks = c(-1, 10, 40, 1000))
  > tmp$sim$DV <- match(cat2, levels(cat2))
  > obj <- vpc_cat(sim = tmp$sim, obs = tmp$obs, vpcdb = TRUE)
  Error in namespaceExport(ns, exports) : 
    undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
  Calls: vpc_cat ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
Running examples in 'vqtl-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.scanonevar
> ### Title: plot.scanonevar
> ### Aliases: plot.scanonevar
> 
> ### ** Examples
> 
> set.seed(27599)
> test.cross <- qtl::sim.cross(map = qtl::sim.map(len = rep(20, 3), n.mar = 5), n.ind = 50)
> test.sov <- scanonevar(cross = test.cross)
calculating genoprobs with stepwidth = 5, off.end = 0, error.prob = 1e-4, map.function = 'haldane'
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: scanonevar ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vqtl_vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'vsgoftest_tutorial.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_dete
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'MultiClassVtreat.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Calculate_WACC_in_R.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_det
Execution halted
package 'stringi' exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Running examples in 'wakefield-Ex.R' failed
The error most likely occurred in:

> ### Name: lorem_ipsum
> ### Title: Generate Random Lorem Ipsum Strings
> ### Aliases: lorem_ipsum paragraph
> ### Keywords: character string
> 
> ### ** Examples
> 
> lorem_ipsum(10)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: lorem_ipsum ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'walkalytics' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: ggplot2
Error: package or namespace load failed for 'walkr' in inDL(x, as.logical(local), as.logical(now), ...):
 ICU init failed: U_FILE_ACCESS_ERROR
Execution halted
** DONE
Running examples in 'wally-Ex.R' failed
The error most likely occurred in:

> ### Name: wallyPlot
> ### Title: Wally plots to assess calibration of a risk or survival
> ###   prediction
> ### Aliases: wallyPlot
> 
> ### ** Examples
> 
> # Survival setting
> library(prodlim)
> library(survival)
> set.seed(180)
> d = SimSurv(180)
> f = coxph(Surv(time,status)~X1+X2,data=d,x=TRUE)
> ## Not run: 
> ##D wallyPlot(f,
> ##D           time=4,
> ##D           q=10,
> ##D           data=d,
> ##D           formula=Surv(time,status)~1)
> ##D  wallyPlot(f,
> ##D           time=4,
> ##D           q=10,
> ##D           hanging=TRUE,
> ##D           data=d,
> ##D           formula=Surv(time,status)~1)
> ## End(Not run)
> 
> # Competing risks setting
> library(prodlim)
> library(survival)
> library(riskRegression)
Loading required package: data.table
Loading required package: ggplot2
Error: package or namespace load failed for 'riskRegression' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_
Execution halted
Running 'Reproduce-Fig-paper.R' [3s]
Running the tests in 'tests/Reproduce-Fig-paper.R' failed.
Complete output:
  > 
  > # {{{ load packages
  > library(survival)
  > library(prodlim)
  > library(riskRegression)
  Loading required package: data.table
  Loading required package: ggplot2
  Error: package or namespace load failed for 'riskRegression' in namespaceExport(ns, exports):
   undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_
  Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'wand' in inDL(x, as.logical(local), as.logical(now), ...):
 ICU init failed: U_FILE_ACCESS_ERROR
Execution halted
** DONE
Loading this package had a fatal error status code 1
Loading log:
Loading required package: maps
Loading required package: tuneR
Loading required package: seewave
Loading required package: NatureSounds
Error: package or namespace load failed for 'warbleR' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'washdata.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Landsat8.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Using_the_wbstats_package.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wCorrArguments.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'basics.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(wdm)
  > 
  > test_check("wdm")
  -- 1. Error: method hoeffding is correct (@test_computations_unweighted.R#24)  -
  ICU init failed: U_FILE_ACCESS_ERROR
  1: expect_equal(wdm(x, method = "hoeffd"), Hmisc::hoeffd(x)$D) at testthat/test_computations_unweighted.R:24
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  -- 2. Error: method hoeffding is correct (@test_computations_unweighted.R#79)  -
  ICU init failed: U_FILE_ACCESS_ERROR
  1: expect_equal(indep_test(x, y, method = "hoeffd")$p_value, Hmisc::hoeffd(x, y)$P[1, 
         2], tol = 0.03) at testthat/test_computations_unweighted.R:79
  2: quasi_label(enquo(expected), expected.label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: Hmisc::hoeffd
  5: getExportedValue(pkg, name)
  6: asNamespace(ns)
  7: getNamespace(ns)
  8: tryCatch(loadNamespace(name), error = function(e) stop(e))
  9: tryCatchList(expr, classes, parentenv, handlers)
  10: tryCatchOne(expr, names, parentenv, handlers[[1L]])
  11: value[[3L]](cond)
  
  == testthat results  ===========================================================
  OK: 73 SKIPPED: 0 FAILED: 2
  1. Error: method hoeffding is correct (@test_computations_unweighted.R#24) 
  2. Error: method hoeffding is correct (@test_computations_unweighted.R#79) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'weathermetrics.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'webchem' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, st
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'webglobe.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'webr' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'weco-vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, s
Execution halted
Error in re-building vignettes:
  ...
Loading required package: grid
Loading required package: Matrix
Loading required package: survival

Attaching package: 'survey'

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

    dotchart

Quitting from lines 97-101 (WeightIt_A0_basic_use.Rmd) 
Error: processing vignette 'WeightIt_A0_basic_use.Rmd' failed with diagnostics:
object 'stats' not found
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: Hmisc
Loading required package: lattice
Loading required package: survival
Loading required package: Formula
Loading required package: ggplot2
Error: package or namespace load failed for 'Hmisc' in inDL(x, as.logical(local), as.logical(now), ...):
 ICU init failed: U_FILE_ACCESS_ERROR
Error: package 'Hmisc' could not be loaded
Execution halted
** DONE
Error in re-building vignettes:
  ...
Error: processing vignette 'wellknown_vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_dete
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'wevid' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wheatmap.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_e
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Whoapi.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Using_widgetframe.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Running examples in 'widyr-Ex.R' failed
The error most likely occurred in:

> ### Name: pairwise_cor
> ### Title: Correlations of pairs of items
> ### Aliases: pairwise_cor pairwise_cor_
> 
> ### ** Examples
> 
> 
> library(dplyr)

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

> library(gapminder)
> 
> gapminder %>%
+   pairwise_cor(country, year, lifeExp)
Error in namespaceExport(ns, exports) : 
  undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_detect2, stri_enc_fromutf32, stri_enc_get, stri_enc_inf
Calls: %>% ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Loading required package: maps
Error: package or namespace load failed for 'wikilake' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wikitaxa_vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detec
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'wildcard' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wildlifeDI-vignette.Rnw' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_det
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wiod.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_d
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'withr.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_enc_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'womblR-example.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, 
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'Introductory-Econometrics-Examples.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_an
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wordcloud.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect, stri_
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wordspace-intro.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'wflow-01-getting-started.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_en
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'worldmet' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, s
Execution halted
Error in re-building vignettes:
  ...
Error: processing vignette 'worrms_vignette.Rmd' failed with diagnostics:
undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_enc_detect,
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    data  12.6Mb
Found the following significant warnings:
  Warning: S3 methods '[.fun_list', '[.grouped_df', 'all.equal.tbl_df', 'anti_join.data.frame', 'anti_join.tbl_df', 'arrange.data.frame', 'arrange.default', 'arrange.grouped_df', 'arrange.tbl_df', 'arrange_.data.frame', 'arrange_.tbl_df', 'as.data.frame.grouped_df', 'as.data.frame.rowwise_df', 'as.data.frame.tbl_cube', 'as.data.frame.tbl_df', 'as.table.tbl_cube', 'as.tbl.data.frame', 'as.tbl.tbl', 'as.tbl_cube.array', 'as.tbl_cube.data.frame', 'as.tbl_cube.matrix', 'as.tbl_cube.table', 'as_data_frame.grouped_df', 'as_data_frame.tbl_cube', 'auto_copy.tbl_cube', 'auto_copy.tbl_df', 'cbind.grouped_df', 'collapse.data.frame', 'collect.data.frame', 'common_by.NULL', 'common_by.character', 'common_by.default', 'common_by.list', 'compute.data.frame', 'copy_to.DBIConnection', 'copy_to.src_local', 'default_missing.data.frame', 'default_missing.default', 'dim.tbl_cube', 'distinct.data.frame', 'distinct.default', 'distinct.grouped_df', 'distinct.tbl_df', 'distinct_.data.frame', 'distinct_.grouped_df', 'dist [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.4/wppExplorer.Rcheck/00install.out' for details.
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'wppExplorer' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any
Execution halted
Loading this package had a fatal error status code 1
Loading log:
Error: package or namespace load failed for 'wql' in namespaceExport(ns, exports):
 undefined exports: %s!=%, %s!==%, %s+%, %s<%, %s<=%, %s==%, %s===%, %s>%, %s>=%, %stri!=%, %stri!==%, %stri+%, %stri<%, %stri<=%, %stri==%, %stri===%, %stri>%, %stri>=%, stri_datetime_add<-, stri_sub<-, stri_subset<-, stri_subset_charclass<-, stri_subset_coll<-, stri_subset_fixed<-, stri_subset_regex<-, stri_c, stri_c_list, stri_cmp, stri_cmp_eq, stri_cmp_equiv, stri_cmp_ge, stri_cmp_gt, stri_cmp_le, stri_cmp_lt, stri_cmp_neq, stri_cmp_nequiv, stri_compare, stri_conv, stri_count, stri_count_boundaries, stri_count_charclass, stri_count_coll, stri_count_fixed, stri_count_regex, stri_count_words, stri_datetime_add, stri_datetime_create, stri_datetime_fields, stri_datetime_format, stri_datetime_fstr, stri_datetime_now, stri_datetime_parse, stri_datetime_symbols, stri_detect, stri_detect_charclass, stri_detect_coll, stri_detect_fixed, stri_detect_regex, stri_dup, stri_duplicated, stri_duplicated_any, stri_e
Execution halted