installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.7Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  fe-protocol2.c:1615:2: warning: 'strncpy' specified bound 32 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1616:2: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
  fe-protocol2.c:1620:3: warning: 'strncpy' specified bound 64 equals destination size [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RPostgreSQL.Rcheck/00install.out' for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   5.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RQDA.Rcheck/00install.out' for details.
installed size is 26.6Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rrepast.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSCAT.Rcheck/00install.out' for details.
Found the following significant warnings:
  cli.c:232:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSclient.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSDA.Rcheck/00install.out' for details.
Found the following significant warnings:
  RSserver.c:64:44: warning: passing argument 4 of 'setsockopt' from incompatible pointer type [-Wincompatible-pointer-types]
   #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/4.0gcc8/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/4.0gcc8/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/4.0gcc8/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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rsgcc.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   3.8Mb
Found the following significant warnings:
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6607 and 7237 may overlap 1 byte at offset 7237 [-Wrestrict]
  kr_io.cpp:891:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
  kr_io.cpp:868:9: warning: 'char* strcat(char*, const char*)' accessing 631 or more bytes at offsets 6719 and 7349 may overlap 1 byte at offset 7349 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RSNNS.Rcheck/00install.out' for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    libs  17.5Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rstap.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.6Mb
Found the following significant warnings:
  RngStreams.c:332:4: warning: 'strncpy' specified bound depends on the length of the source argument [-Wstringop-overflow=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/rstream.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rsubgroup.Rcheck/00install.out' for details.
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) (2019-11-14 r77415)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows Server 2008 x64 (build 6003) 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_4.0.0
> 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  9.3Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rSymPy.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rtextrankr.Rcheck/00install.out' for details.
Found the following significant warnings:
  bgc_hmm.c:241:15: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  bgc_hmm.c:242:13: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  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 'd:/Rcompile/CRANpkg/local/4.0v3/rtfbs.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       2.3Mb
    projects   2.7Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RtutoR.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RunuranGUI.Rcheck/00install.out' for details.
Found the following significant warnings:
  vcglib/wrap/ply/plylib.cpp:3666:14: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/Rvcg.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/rviewgraph.Rcheck/00install.out' for details.
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    include   2.5Mb
    libs      8.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RWekajars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RWeka.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/RxnSim.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Error(s) in re-building vignettes:
--- re-building 'RxODE-intro.Rmd' using rmarkdown
Quitting from lines 36-47 (RxODE-intro.Rmd) 
Error: processing vignette 'RxODE-intro.Rmd' failed with diagnostics:
Error building model
--- failed re-building 'RxODE-intro.Rmd'

--- re-building 'RxODE-syntax.Rmd' using rmarkdown
--- finished re-building 'RxODE-syntax.Rmd'

SUMMARY: processing the following file failed:
  'RxODE-intro.Rmd'

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building 'introduction.Rmd' using rmarkdown
--- finished re-building 'introduction.Rmd'

--- re-building 'sentiment.Rmd' using rmarkdown

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 44-46 (sentiment.Rmd) 
Error: processing vignette 'sentiment.Rmd' failed with diagnostics:
SSL certificate problem: unable to get local issuer certificate
--- failed re-building 'sentiment.Rmd'

SUMMARY: processing the following file failed:
  'sentiment.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   2.3Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    help   3.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SanzCircos.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         1.5Mb
    extdata   1.3Mb
    libs      2.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SBRect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/scagnostics.Rcheck/00install.out' for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   2.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   4.0Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SeqGrapheR.Rcheck/00install.out' for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   3.6Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
    libs   2.0Mb
installed size is 95.5Mb
  sub-directories of 1Mb or more:
    doc     12.0Mb
    gdal     3.9Mb
    libs    70.6Mb
    proj     5.0Mb
    sqlite   1.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   3.3Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SimuChemPC.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/sjdbc.Rcheck/00install.out' for details.
Found the following significant warnings:
  slfm_MDN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
  slfm_MNN.cpp:26:40: warning: left operand of comma operator has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/slfm.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/smartR.Rcheck/00install.out' for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.1Mb
Running 'testthat.R' [86s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(smooth)
  Loading required package: greybox
  Package "greybox", v0.5.6 loaded.
  This is package "smooth", v2.5.4
  > 
  > test_check("smooth")
  -- 1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40)  --
  suppressWarnings(testModel$xreg) is not null.
  
  == testthat results  ===========================================================
  [ OK: 72 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Select exogenous variables for GUMX on N1457 (@test_ges.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  createPosDef.cpp:84:13: warning: statement has no effect [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/smoothSurv.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   2.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/sonicscrewdriver.Rcheck/00install.out' for details.
Running 'test-all.R' [183s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > test_check("SpaDES.core")
  Loading required package: SpaDES.core
  Loading required package: quickPlot
  Loading required package: reproducible
  
  Attaching package: 'SpaDES.core'
  
  The following objects are masked from 'package:stats':
  
      end, start
  
  The following object is masked from 'package:utils':
  
      citation
  
  -- 1. Error: test cache (@test-cache.R#34)  ------------------------------------
  is.character(repoDir) & length(repoDir) == 1 is not TRUE
  Backtrace:
   1. reproducible::showCache(sims[[1]])
   2. reproducible::showCache(sims[[1]])
   6. archivist::showLocalRepo(x)
   7. base::stopifnot(is.character(repoDir) & length(repoDir) == 1)
  
  [1] "<environment: 0x0000000029a26c08>"
  [1] "<environment: 0x000000001f2e6c30>"
  -- 2. Error: 3 levels of parent and child modules load and show correctly (@test
  object 'from' not found
  Backtrace:
   1. SpaDES.core::moduleGraph(mySim, FALSE)
   2. SpaDES.core::moduleGraph(mySim, FALSE)
   3. base::lapply(parents, function(par) data.frame(el[from == par]))
   4. SpaDES.core:::FUN(X[[i]], ...)
   7. base::`[.data.frame`(el, from == par)
  
  == testthat results  ===========================================================
  [ OK: 469 | SKIPPED: 9 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: test cache (@test-cache.R#34) 
  2. Error: 3 levels of parent and child modules load and show correctly (@test-module-deps-methods.R#202) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   2.8Mb
Found the following significant warnings:
  fft.c:138:9: warning: array subscript -1 is below array bounds of 'int[15]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SpatialExtremes.Rcheck/00install.out' for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   2.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/spatsurv.Rcheck/00install.out' for details.
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   3.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/spcosa.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   2.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    libs   2.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   3.1Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SqlRender.Rcheck/00install.out' for details.
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 'd:/Rcompile/CRANpkg/local/4.0gcc8/SSN.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/stacomiR.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    include   9.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   2.5Mb
Found the following significant warnings:
  MaxChi.c:468:20: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
  Phylpro.c:457:24: warning: passing argument 1 to restrict-qualified parameter aliases with argument 3 [-Wrestrict]
See 'd:/Rcompile/CRANpkg/local/4.0v3/stepwise.Rcheck/00install.out' for details.
Running examples in 'stepwise-Ex.R' failed
The error most likely occurred in:

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


	demo(phylpro)
	---- ~~~~~~~

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

> breaks<-c(548, 735, 832)

> WinHalfWidth<-30

> permReps<-10

> b<-phylpro(inputFile, breaks, WinHalfWidth, permReps)

> summary.phylpro(b)
Error in siteChisqs[1] <- object$corrs[1] : replacement has length zero
Calls: demo ... source -> withVisible -> eval -> eval -> summary.phylpro
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   2.1Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/streamMOA.Rcheck/00install.out' for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
Found the following significant warnings:
  icu61/common/cstring.h:43:70: warning: 'char* strncpy(char*, const char*, size_t)' output truncated before terminating nul copying as many bytes from a string as its length [-Wstringop-truncation]
See 'd:/Rcompile/CRANpkg/local/4.0v3/stringi.Rcheck/00install.out' for details.
installed size is 35.6Mb
  sub-directories of 1Mb or more:
    libs  34.8Mb
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type 'class std::runtime_error' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/strum.Rcheck/00install.out' for details.
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type 'struct subprocess::subprocess_exception' by value [-Wcatch-value=]
See 'd:/Rcompile/CRANpkg/local/4.0v3/subprocess.Rcheck/00install.out' for details.
Running 'testthat.R' [132s]
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
  Backtrace:
   1. testthat::expect_true(process_exists(child_id))
   4. subprocess::process_exists(child_id)
   5. base::isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  [ OK: 58 | SKIPPED: 3 | WARNINGS: 0 | 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' [131s]
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
  Backtrace:
   1. testthat::expect_true(process_exists(child_id))
   4. subprocess::process_exists(child_id)
   5. base::isTRUE(.Call("C_process_exists", as.integer(x)))
  
  == testthat results  ===========================================================
  [ OK: 58 | SKIPPED: 3 | WARNINGS: 0 | 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
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/subspace.Rcheck/00install.out' for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   2.2Mb
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  14.1Mb
Found the following significant warnings:
  lineariadmm.c:189:17: warning: value computed is not used [-Wunused-value]
  lineariadmm.c:190:17: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/svmadmm.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: GNU Extension: Nonstandard type declaration REAL*8 at (1)
  Warning: GNU Extension: Different type kinds at (1)
  Warning: GNU Extension: initialization of common block variable 'iset' in DATA statement at (1)
  Warning: GNU Extension: Variable 'iset' at (1) is in COMMON but only in BLOCK DATA initialization is allowed
  Warning: GNU Extension: Missing comma at (1)
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/SWATmodel.Rcheck/00install.out' for details.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/table1xls.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tabulizerjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tabulizer.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    3.9Mb
    libs   2.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   3.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs   3.2Mb
installed size is 29.1Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs      13.9Mb
    tessdata  14.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   2.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
Found the following significant warnings:
  D:/RCompile/CRANpkg/lib/4.0v3/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]
  D:/RCompile/CRANpkg/lib/4.0v3/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 'd:/Rcompile/CRANpkg/local/4.0v3/text2vec.Rcheck/00install.out' for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    doc    3.6Mb
    libs   2.6Mb
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.02    0.00    2.03 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11425 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.02    0.00    2.42 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11474 (sockconn)
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/textmining.Rcheck/00install.out' for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   2.9Mb
    libs      2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs         2.2Mb
    references   1.1Mb
Found the following significant warnings:
  lmdb/mdb.c:1734:2: warning: array subscript 8192 is above array bounds of 'char[5120]' [-Warray-bounds]
See 'd:/Rcompile/CRANpkg/local/4.0v3/thor.Rcheck/00install.out' for details.
installed size is 23.1Mb
  sub-directories of 1Mb or more:
    examples  19.5Mb
    include    2.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/tm.plugin.webmining.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc    3.5Mb
    libs   2.0Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  11.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/TSsdmx.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 'd:/Rcompile/CRANpkg/local/4.0gcc8/TukeyRegion.Rcheck/00install.out' for details.
Running examples in 'UCSCXenaTools-Ex.R' failed
The error most likely occurred in:

> ### Name: fetch
> ### Title: Fetch Data from UCSC Xena Hosts
> ### Aliases: fetch fetch_dense_values fetch_dataset_samples
> ###   fetch_dataset_identifiers has_probeMap
> 
> ### ** Examples
> 
> library(UCSCXenaTools)
> 
> host <- "https://toil.xenahubs.net"
> dataset <- "tcga_RSEM_gene_tpm"
> samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
> probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
> genes <- c("TP53", "RB1", "PIK3CA")
> 
> # Fetch samples
> fetch_dataset_samples(host, dataset, 2)
[1] "TCGA-19-1787-01" "TCGA-S9-A7J2-01"
> # Fetch identifiers
> # Fetch expression value by probes
> fetch_dense_values(host, dataset, probes, samples, check = FALSE)
Error in UCSCXenaTools:::.xena_post(host, UCSCXenaTools:::.call(xquery,  : 
  Internal Server Error (HTTP 500).
Calls: fetch_dense_values -> .p_dataset_fetch -> <Anonymous> -> stop_for_status
Execution halted
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs        4.7Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   2.6Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   2.8Mb
Found the following significant warnings:
  libunrtf/my_iconv.c:56:18: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
  libunrtf/my_iconv.c:149:27: warning: passing argument 2 of 'libiconv' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0v3/unrtf.Rcheck/00install.out' for details.
Found the following significant warnings:
  gen_uuid.c:309:11: warning: ordered comparison of pointer with integer zero [-Wpedantic]
See 'd:/Rcompile/CRANpkg/local/4.0v3/uuid.Rcheck/00install.out' for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.1Mb
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 'd:/Rcompile/CRANpkg/local/4.0v3/validatejsonr.Rcheck/00install.out' for details.
installed size is 79.7Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    gdal      3.8Mb
    libs     69.4Mb
    proj      5.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/venneuler.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/VIMGUI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/vmsbase.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/vortexR.Rcheck/00install.out' for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    doc   11.9Mb
    libs   2.1Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    libs   2.2Mb
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 'd:/Rcompile/CRANpkg/local/4.0gcc8/WhopGenome.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/WMCapacity.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/wordnet.Rcheck/00install.out' for details.
Found the following significant warnings:
  assp/dsputils.c:414:13: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/wrassp.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/x12GUI.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/4.0v3/x13binary.Rcheck/00install.out' for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XLConnectJars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XLConnect.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/xlsxjars.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/4.0v3/xlsx.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
Found the following significant warnings:
  RSDTD.c:298:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
  RSDTD.c:372:23: warning: passing argument 2 of 'xmlHashScan' from incompatible pointer type [-Wincompatible-pointer-types]
See 'd:/Rcompile/CRANpkg/local/4.0gcc8/XML.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      2.1Mb
Found the following significant warnings:
  emitter.c:28:6: warning: value computed is not used [-Wunused-value]
See 'd:/Rcompile/CRANpkg/local/4.0v3/yaml.Rcheck/00install.out' for details.
Dependence on R version ‘3.4.2’ not with patchlevel 0
Found the following significant warnings:
  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-patched-gcc/Work/PKGS/audio.Rcheck/00install.out’ for details.
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-patched-gcc/Work/PKGS/bayesCL.Rcheck/00install.out’ for details.
Dependence on R version ‘3.4.1’ not with patchlevel 0
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-patched-gcc/Work/PKGS/BayHap.Rcheck/00install.out’ for details.
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-patched-gcc/Work/PKGS/C50.Rcheck/00install.out’ for details.
---- unloading

 *** caught segfault ***
address 0x7fc2f59ceba0, cause 'invalid permissions'
An irrecoverable exception occurred. R is aborting now ...
Segmentation fault
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘ChainLadder.Rnw’ using Sweave

Welcome to ChainLadder version 0.2.10

Type vignette('ChainLadder', package='ChainLadder') to access
the overall package documentation.

See demo(package='ChainLadder') for a list of demos.

More information is available on the ChainLadder project web-site:
https://github.com/mages/ChainLadder

To suppress this message use:
suppressPackageStartupMessages(library(ChainLadder))

Loading required package: systemfit
Loading required package: Matrix
Loading required package: car
Loading required package: carData
Loading required package: lmtest
Loading required package: zoo

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric


Please cite the 'systemfit' package as:
Arne Henningsen and Jeff D. Hamann (2007). systemfit: A Package for Estimating Systems of Simultaneous Equations in R. Journal of Statistical Software 23(4), 1-40. http://www.jstatsoft.org/v23/i04/.

If you have questions, suggestions, or comments regarding the 'systemfit' package, please use a forum or 'tracker' at systemfit's R-Forge site:
https://r-forge.r-project.org/projects/systemfit/

Error: processing vignette 'ChainLadder.Rnw' failed with diagnostics:
 chunk 58 
Error in `[<-`(`*tmp*`, i, j, value = value[[y]]) : 
  subscript out of bounds

--- failed re-building ‘ChainLadder.Rnw’

SUMMARY: processing the following file failed:
  ‘ChainLadder.Rnw’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [25s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(circumplex)
  > 
  > test_check("circumplex")
  ── 1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17)  ─
  `qb` not equivalent to as_radian(as_degree(c(180, 225, 270, 315, 0))).
  1/5 mismatches
  [5] 6.28 - 0 == 6.28
  
  ── 2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27)  ─
  `qb` not equivalent to as_radian(as_degree(c(270, 315, 0, 45, 90))).
  1/5 mismatches
  [3] 6.28 - 0 == 6.28
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 204 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17) 
  2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(clusternomics)
  > 
  > test_check("clusternomics")
  Killed
Running ‘test.R’ [183s/111s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  ── 1. Error: arguments are checked (@testAnalysis.R#12)  ───────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: arguments are checked (@testData.R#532)  ──────────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘countToFPKM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fpkmheatmap
> ### Title: Convert Counts to Fragments per Kilobase of Transcript per
> ###   Million (FPKM) A FPKM heatmap plot of the highly variable features in
> ###   RNA-Seq dataset
> ### Aliases: fpkmheatmap
> 
> ### ** Examples
> 
> library(countToFPKM)
> 
> file.readcounts <- system.file("extdata", "RNA-seq.read.counts.csv", package="countToFPKM")
> file.annotations <- system.file("extdata", "Biomart.annotations.hg38.txt", package="countToFPKM")
> file.sample.metrics <- system.file("extdata", "RNA-seq.samples.metrics.txt", package="countToFPKM")
> 
> 
> # Import the read count matrix data into R.
> counts <- as.matrix(read.csv(file.readcounts))
> 
> # Import feature annotations. 
> # Assign feature length into a numeric vector.
> gene.annotations <- read.table(file.annotations, sep="\t", header=TRUE)
> featureLength <- gene.annotations$length
> 
> # Import sample metrics. 
> # Assign mean fragment length into a numeric vector.
> samples.metrics <- read.table(file.sample.metrics, sep="\t", header=TRUE)
> meanFragmentLength <- samples.metrics$meanFragmentLength
> 
> # Return FPKM into a numeric matrix.
> fpkm_matrix <- fpkm (counts, featureLength, meanFragmentLength)
> 
> # Plot log10(FPKM+1) heatmap of top 30 highly variable features
> fpkmheatmap(fpkm_matrix, topvar=30, showfeaturenames=TRUE, return_log = TRUE)
Error in NextMethod("[[") : 
  getter call used outside of a complex assignment.
Calls: <Anonymous> ... adj_dend -> adj_dend -> [[ -> [[.dendrogram -> NextMethod
Execution halted
Running examples in ‘covatest-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: read.STdata
> ### Title: Imports a text file in R
> ### Aliases: read.STdata
> 
> ### ** Examples
> 
> #example 1: import a text file, with dates stored in a single column (the 4th)
> # and fill missing time points in monthly time series, with time lag equal to one
> 
> file_date <- system.file("extdata", "file_date.txt", package = "covatest")
> db.date <- read.STdata(file = file_date, header = TRUE, iclx = 2, icly = 3, iclt = 0,
+ icldate = c(icl.date = 4, iclty = 0, icltm = 0, icltd = 0),
+ icltime = c(icl.time = 0, icltH =0, icltM = 0, icltS = 0),
+ iclvr = 5, iclsp = 1, missing.v = -99999, save.as = "data.frame",
+ date.format = c("Date", "%d-%m-%Y"), bytime = "%m", tlag = 1)
Error in seq.Date(from = as.Date(t1), to = as.Date(t2), by = "month") : 
  'from' must be of length 1
Calls: read.STdata -> seq -> seq.Date
Execution halted
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-patched-gcc/Work/PKGS/Cubist.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘dataone-federation.Rmd’ using rmarkdown
--- finished re-building ‘dataone-federation.Rmd’

--- re-building ‘dataone-overview.Rmd’ using rmarkdown
--- finished re-building ‘dataone-overview.Rmd’

--- re-building ‘download-data.Rmd’ using rmarkdown
--- finished re-building ‘download-data.Rmd’

--- re-building ‘known-issues.Rmd’ using rmarkdown
--- finished re-building ‘known-issues.Rmd’

--- re-building ‘searching-dataone.Rmd’ using rmarkdown
--- finished re-building ‘searching-dataone.Rmd’

--- re-building ‘update-package.Rmd’ using rmarkdown
Quitting from lines 48-56 (update-package.Rmd) 
Error: processing vignette 'update-package.Rmd' failed with diagnostics:
too few arguments
--- failed re-building ‘update-package.Rmd’

--- re-building ‘upload-data.Rmd’ using rmarkdown
--- finished re-building ‘upload-data.Rmd’

SUMMARY: processing the following file failed:
  ‘update-package.Rmd’

Error: Vignette re-building failed.
Execution halted
DEMIPathway: no visible global function definition for ‘dhyper’
DEMIPathway: no visible global function definition for ‘p.adjust’
calcHypergeoExon: no visible global function definition for ‘dhyper’
calcHypergeoProb: no visible global function definition for ‘dhyper’
demi: no visible global function definition for ‘write.table’
demi.t.test: no visible global function definition for ‘t.test’
demi.wilcox.test: no visible global function definition for
  ‘wilcox.test’
demi.wilcox.test.fast: no visible global function definition for
  ‘wilcox.test’
demiequal: no visible global function definition for ‘wilcox.test’
wprob: no visible global function definition for ‘combn’
diffexp,DEMIDiff: no visible global function definition for ‘median’
diffexp,DEMIDiff: no visible global function definition for ‘p.adjust’
loadAnnotation,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadBlat,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadCytoband,DEMIExperiment-environment: no visible global function
  definition for ‘data’
loadPathway,DEMIExperiment-environment: no visible global function
  definition for ‘data’
Undefined global functions or variables:
  combn data dhyper median p.adjust t.test wilcox.test write.table
Consider adding
  importFrom("stats", "dhyper", "median", "p.adjust", "t.test",
             "wilcox.test")
  importFrom("utils", "combn", "data", "write.table")
to your NAMESPACE file.
Running ‘test-all.R’ [27s/29s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  ── 1. Failure: extract au (@test-pvclust_extract.R#12)  ────────────────────────
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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-patched-gcc/Work/PKGS/dggridR.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-patched-gcc/Work/PKGS/dpglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘eclust.Rmd’ using rmarkdown
See example usage at http://sahirbhatnagar.com/eclust/
Quitting from lines 470-471 (eclust.Rmd) 
Error: processing vignette 'eclust.Rmd' failed with diagnostics:
getter call used outside of a complex assignment.
--- failed re-building ‘eclust.Rmd’

SUMMARY: processing the following file failed:
  ‘eclust.Rmd’

Error: Vignette re-building failed.
Execution halted
Rd file 'mosaicPermDialog.Rd':
  \usage lines wider than 90 characters:
                                                             displayPermCommand=TRUE, extendedOptions=TRUE)
     setMosaicPalette(palettename,reverse=FALSE)                                                     

These lines will be truncated in the PDF manual.
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-patched-gcc/Work/PKGS/epanet2toolkit.Rcheck/00install.out’ for details.
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-patched-gcc/Work/PKGS/FastRWeb.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Killed
Rd file 'POICalc.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'POIcoords_-.Rd':
  \examples lines wider than 100 characters:
        irisPOI@wordsInQuery <- c('high.Sepal.Length', 'high.Sepal.Width', 'high.Petal.Length', 'high.Petal.Width',
                                  'low.Sepal.Length', 'low.Sepal.Width', 'low.Petal.Length', 'low.Petal.Width')

Rd file 'plotPOI.Rd':
  \examples lines wider than 100 characters:
          graphPOI@docs <- matrix(c(seq(1:nrow(graphPOI@objeto)), seq(1:nrow(graphPOI@objeto))), ncol = 2)
        graphPOI@objeto <- graphPOI@objeto <- rbind(c(0,.05), c(.05,0), c(0,-.05), c(-.05,0) ,round(circulo(0,0,.3,PLOT = FALSE),2))
         1 - (max(USArrests[,4]) - USArrests[,4]) / (max(max(USArrests[,4]) - USArrests[,4])),                                               ... [TRUNCATED]
        usaPOI@wordsInQuery <- c(paste('High', names(USArrests[,c(1,2,4)])), paste('Low', names(USArrests[,c(1,2,4)])))

These lines will be truncated in the PDF manual.
opc : <anonymous>: no visible global function definition for
  ‘parseWorkspace’
opc : <anonymous>: no visible global function definition for
  ‘closeWorkspace’
Undefined global functions or variables:
  closeWorkspace parseWorkspace
Running ‘testthat.R’ [144s/157s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  ── 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  ──────────────
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
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-patched-gcc/Work/PKGS/freeknotsplines.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-patched-gcc/Work/PKGS/gdm.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: ‘__var_41_mma.offset’ is used uninitialized in this function [-Wuninitialized]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gglasso.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown

Attaching package: 'gglogo'

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

    fortify

Killed
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gqlr.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MPG_algorithm.Rmd’ using rmarkdown
Warning in get_engine(options$engine) :
  Unknown language engine 'cpp' (must be registered via knit_engines$set()).
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.248 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

Error: processing vignette 'MPG_algorithm.Rmd' failed with diagnostics:
Failed to compile MPG_algorithm.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See MPG_algorithm.log for more info.
--- failed re-building ‘MPG_algorithm.Rmd’

--- re-building ‘grainscape_vignette.Rmd’ using rmarkdown
--- finished re-building ‘grainscape_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘MPG_algorithm.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘import.Rnw’ using Sweave
Loading required package: XML
GPL Ghostscript 9.50: Unrecoverable error, exit code 1

Error: processing vignette 'import.Rnw' failed with diagnostics:
 chunk 5 (label = chesspiece) 
Error in PostScriptTrace("chess_game_01.fromInkscape.eps") : 
  status 1 in running command 'gs -q -dBATCH -dNOPAUSE -sDEVICE=ps2write -sOutputFile=/dev/null -sstdout=chess_game_01.fromInkscape.eps.xml /tmp/Rtmp0mevMC/file600939d35468.ps'

--- failed re-building 'import.Rnw'

--- re-building ‘importText.Rnw’ using Sweave
Loading required package: XML
GPL Ghostscript 9.50: Unrecoverable error, exit code 1

Error: processing vignette 'importText.Rnw' failed with diagnostics:
 chunk 4 (label = simpleimport) 
Error in PostScriptTrace("hello.ps", "hello.xml") : 
  status 1 in running command 'gs -q -dBATCH -dNOPAUSE -sDEVICE=ps2write -sOutputFile=/dev/null -sstdout=hello.xml /tmp/Rtmp3rFVQi/file62be45413f50.ps'

--- failed re-building 'importText.Rnw'

SUMMARY: processing the following files failed:
  ‘import.Rnw’ ‘importText.Rnw’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/gwsem.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-patched-gcc/Work/PKGS/hier.part.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘simu.Rmd’ using rmarkdown
Killed
Running examples in ‘huxtable-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: add_footnote
> ### Title: Add a row with a footnote
> ### Aliases: add_footnote
> 
> ### ** Examples
> 
> jams <- add_footnote(jams,
+       "* subject to availability")
Error in touched[da_rows, da_cols] : subscript out of bounds
Calls: add_footnote ... colspan<-.huxtable -> check_span_shadows -> display_cells
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘design-principles.Rmd’ using rmarkdown
--- finished re-building ‘design-principles.Rmd’

--- re-building ‘huxreg.Rmd’ using rmarkdown
Quitting from lines 51-53 (huxreg.Rmd) 
Error: processing vignette 'huxreg.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘huxreg.Rmd’

--- re-building ‘huxtable.Rmd’ using rmarkdown

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: 'huxtable'

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

    add_rownames

Quitting from lines 42-43 (huxtable.Rmd) 
Error: processing vignette 'huxtable.Rmd' failed with diagnostics:
Overlapping multirow/multicolumn cells in [1, 3] of huxtableOverlapping multirow/multicolumn cells in [1, 4] of huxtable
--- failed re-building ‘huxtable.Rmd’

--- re-building ‘themes.Rmd’ using rmarkdown
--- finished re-building ‘themes.Rmd’

SUMMARY: processing the following files failed:
  ‘huxreg.Rmd’ ‘huxtable.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [124s/135s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Error: as_huxtable.sim_margins works (@test_sim_margins.R#110)  ──────────
  subscript out of bounds
  Backtrace:
    1. testthat::expect_is(as_huxtable.sim_margins(ss3), "huxtable")
    4. interactions:::as_huxtable.sim_margins(ss3)
    5. interactions:::make_table(...)
    6. huxtable::insert_row(tab, c(lab, rep(NA, col_mult)), after = row)
    8. huxtable:::`colspan<-.huxtable`(`*tmp*`, value = `*vtmp*`)
    9. huxtable:::check_span_shadows(ht, "col", value)
   10. huxtable:::display_cells(ht, new_colspan = value)
  
  ── 2. Error: as_huxtable.sim_slopes works (@test_sim_slopes.R#77)  ─────────────
  subscript out of bounds
  Backtrace:
    1. testthat::expect_is(as_huxtable.sim_slopes(ss3), "huxtable")
    4. interactions:::as_huxtable.sim_slopes(ss3)
    5. interactions:::make_table(...)
    6. huxtable::insert_row(tab, c(lab, rep(NA, col_mult)), after = row)
    8. huxtable:::`colspan<-.huxtable`(`*tmp*`, value = `*vtmp*`)
    9. huxtable:::check_span_shadows(ht, "col", value)
   10. huxtable:::display_cells(ht, new_colspan = value)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 159 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: as_huxtable.sim_margins works (@test_sim_margins.R#110) 
  2. Error: as_huxtable.sim_slopes works (@test_sim_slopes.R#77) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘categorical.Rmd’ using rmarkdown
--- finished re-building ‘categorical.Rmd’

--- re-building ‘interactions.Rmd’ using rmarkdown
Warning: 0 is outside the observed range of Murder
Warning: 0 is outside the observed range of Murder
Warning: 0 is outside the observed range of Murder

Attaching package: 'huxtable'

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

    theme_grey

Quitting from lines 413-417 (interactions.Rmd) 
Error: processing vignette 'interactions.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘interactions.Rmd’

SUMMARY: processing the following file failed:
  ‘interactions.Rmd’

Error: Vignette re-building failed.
Execution halted
Rd file 'N2.cohen.kappa.Rd':
  \examples lines wider than 100 characters:
       N2.cohen.kappa(c(0.2, 0.25, 0.55), k1=0.6, k0=0.4)                                                            

These lines will be truncated in the PDF manual.
Dependence on R version ‘3.4.4’ not with patchlevel 0
Running examples in ‘jtools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: export_summs
> ### Title: Export regression summaries to tables
> ### Aliases: export_summs
> 
> ### ** Examples
> 
> states <- as.data.frame(state.x77)
> fit1 <- lm(Income ~ Frost, data = states)
> fit2 <- lm(Income ~ Frost + Illiteracy, data = states)
> fit3 <- lm(Income ~ Frost + Illiteracy + Murder, data = states)
> 
> if (requireNamespace("huxtable")) {
+   # Export all 3 regressions with "Model #" labels,
+   # standardized coefficients, and robust standard errors
+   export_summs(fit1, fit2, fit3,
+                model.names = c("Model 1","Model 2","Model 3"),
+                coefs = c("Frost Days" = "Frost",
+                          "% Illiterate" = "Illiteracy",
+                          "Murder Rate" = "Murder"),
+                scale = TRUE, robust = TRUE)
+ }
Loading required namespace: huxtable
Error in touched[da_rows, da_cols] : subscript out of bounds
Calls: export_summs ... colspan<-.huxtable -> check_span_shadows -> display_cells
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/lolog.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MLTA_Gollini_2019.Rmd’ using rmarkdown
Loading required package: MASS
Loading required package: ergm
Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
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.


ergm: version 3.10.4, created on 2019-06-10
Copyright (c) 2019, Mark S. Handcock, University of California -- Los Angeles
                    David R. Hunter, Penn State University
                    Carter T. Butts, University of California -- Irvine
                    Steven M. Goodreau, University of Washington
                    Pavel N. Krivitsky, University of Wollongong
                    Martina Morris, University of Washington
                    with contributions from
                    Li Wang
                    Kirk Li, University of Washington
                    Skye Bender-deMoll, University of Washington
                    Chad Klumb
Based on "statnet" project software (statnet.org).
For license and citation information see statnet.org/attribution
or type citation("ergm").

NOTE: Versions before 3.6.1 had a bug in the implementation of the bd()
constriant which distorted the sampled distribution somewhat. In
addition, Sampson's Monks datasets had mislabeled vertices. See the
NEWS and the documentation for more details.

NOTE: Some common term arguments pertaining to vertex attribute and
level selection have changed in 3.10.0. See terms help for more
details. Use 'options(ergm.term=list(version="3.9.4"))' to use old
behavior.

Killed
Running ‘testthat.R’ [19s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(manhplot)
  > 
  > test_check("manhplot")
  ── 1. Error: Run the manhplusplot function with default params (@testmanhplusplo
  missing value where TRUE/FALSE needed
  Backtrace:
   1. manhplot::manhplusplot(...)
   2. ggplot2::scale_fill_gradientn(...)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
  
  ── 2. Error: Run the manhplusplot function with output as tiff file (@testmanhpl
  missing value where TRUE/FALSE needed
  Backtrace:
   1. manhplot::manhplusplot(...)
   2. ggplot2::scale_fill_gradientn(...)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Run the manhplusplot function with default params (@testmanhplusplot.R#9) 
  2. Error: Run the manhplusplot function with output as tiff file (@testmanhplusplot.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(matrixTests)
  > 
  > test_check("matrixTests")
  Killed
Running ‘mpost.R’ [1s/2s]
  Running ‘path.R’ [1s/1s]
Running the tests in ‘tests/mpost.R’ failed.
Complete output:
  > 
  > library(metapost)
  
  Attaching package: 'metapost'
  
  The following object is masked from 'package:stats':
  
      cycle
  
  The following object is masked from 'package:base':
  
      dir
  
  > library(grid)
  > p <- knot(0, 0) + dir(45) + dir(0:9*-10) + knot(unit(6, "cm"), 0)
  > metapost(p, "fig.mp")
  > mpost("fig.mp", tracing=TRUE)
  This is MetaPost, version 2.00 (TeX Live 2019/Debian) (kpathsea version 6.3.1)
  (/usr/share/texlive/texmf-dist/metapost/base/mpost.mp
  (/usr/share/texlive/texmf-dist/metapost/base/plain.mp
  Preloading the plain mem file, version 1.005) ) (./fig.mp [1] )
  (see the transcript file for additional information)
  1 output file written: fig.1
  Transcript written on fig.log.
  > 
  > controls <- mptrace("fig.log")
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  Read 8 items
  > 
  > library(grImport)
  Loading required package: XML
  > PostScriptTrace("fig.1")
  GPL Ghostscript 9.50: Unrecoverable error, exit code 1
  Error in PostScriptTrace("fig.1") : 
    status 1 in running command 'gs -q -dBATCH -dNOPAUSE -sDEVICE=ps2write -sOutputFile=/dev/null -sstdout=fig.1.xml /tmp/Rtmppw73zf/file16e4559f0623.ps'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Killed
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-patched-gcc/Work/PKGS/MigClim.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘How_to_use_mvMORPH.Rmd’ using rmarkdown
Loading required package: phytools
Loading required package: ape
Loading required package: maps
Loading required package: corpcor
Loading required package: subplex
##
## mvMORPH package (1.1.0)
## Multivariate evolutionary models
##
## See the tutorials: browseVignettes("mvMORPH")
##
## To cite package 'mvMORPH': citation("mvMORPH")
##
Done.
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
Efficient parameterization is not yet implemented for user-defined constraints
Please check the results carefully!!
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.137 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

Error: processing vignette 'How_to_use_mvMORPH.Rmd' failed with diagnostics:
Failed to compile How_to_use_mvMORPH.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See How_to_use_mvMORPH.log for more info.
--- failed re-building ‘How_to_use_mvMORPH.Rmd’

--- re-building ‘tutorial_mvMORPH.Rmd’ using rmarkdown
Done.
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.133 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

Error: processing vignette 'tutorial_mvMORPH.Rmd' failed with diagnostics:
Failed to compile tutorial_mvMORPH.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See tutorial_mvMORPH.log for more info.
--- failed re-building ‘tutorial_mvMORPH.Rmd’

SUMMARY: processing the following files failed:
  ‘How_to_use_mvMORPH.Rmd’ ‘tutorial_mvMORPH.Rmd’

Error: Vignette re-building failed.
Execution halted
Dependence on R version ‘3.4.3’ not with patchlevel 0
Found the following significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/odbc.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘discrete.Rmd’ using rmarkdown
Quitting from lines 269-272 (discrete.Rmd) 
Error: processing vignette 'discrete.Rmd' failed with diagnostics:
Error compiling source
--- failed re-building ‘discrete.Rmd’

--- re-building ‘odin.Rmd’ using rmarkdown
--- finished re-building ‘odin.Rmd’

SUMMARY: processing the following file failed:
  ‘discrete.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Rd file 'dmes.Rd':
  \examples lines wider than 100 characters:
     > #cf. Efron, B. & Tibshirani (1993). An Introduction to the Bootstrap. New York/London: Chapman&Hall.
     > #Ruscio, J. & Mullen, T. (2012). Confidence Intervals for the Probability of Superiority Effect Size Measure and the Area Under a Rec ... [TRUNCATED]

Rd file 'orddom_f.Rd':
  \examples lines wider than 100 characters:
     orddom_f(con_pre,ex_pre,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 01")   
     orddom_f(con_post,ex_post,alpha=0.025,decimalpt=",",description="EXP 01: Between groups at time 02") 
     orddom_f(ex_pre,ex_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within exp 01 to 02") 
     orddom_f(con_pre,con_post,alpha=0.025,paired=TRUE,decimalpt=",",description="EXP 01: Within con 01 to 02") 

These lines will be truncated in the PDF manual.
Rd file 'CalGIF.Rd':
  \examples lines wider than 100 characters:
     ###calculate the global influence factor (GIF) by using the random walk with restart (RWR) algorithm###
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 
     #Each element is the GIF score and whose name correspond to gene symbol in the gene expression data. 

Rd file 'PAGI.Main.Rd':
  \examples lines wider than 100 characters:
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",
     #Its columns include "Gene number in the (sorted) pathway", "gene symbol from the gene express data",
     #"location of the gene in the sorted gene list", "the T-score of gene between two biological states",

These lines will be truncated in the PDF manual.
Running examples in ‘pds3-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: pds3_lexer_parser
> ### Title: Access PDS3 Lexer & Parser
> ### Aliases: pds3_lexer_parser
> 
> ### ** Examples
> 
> util <- pds3_lexer_parser()
Error in Productions[[p$number + 1]] : 
  attempt to select more than one element in get1index <real>
Calls: pds3_lexer_parser ... <Anonymous> -> <Anonymous> -> <Anonymous> -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pds3.Rmd’ using rmarkdown
Quitting from lines 67-70 (pds3.Rmd) 
Error: processing vignette 'pds3.Rmd' failed with diagnostics:
attempt to select more than one element in get1index <real>
--- failed re-building ‘pds3.Rmd’

SUMMARY: processing the following file failed:
  ‘pds3.Rmd’

Error: Vignette re-building failed.
Execution halted
Rd file 'envelopeArea_and_Perimeter.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")

Rd file 'generateEnvelope.Rd':
  \examples lines wider than 100 characters:
     cat("envelope area = ", envelopeStats["area"], " perimeter = ", envelopeStats["perimeter"],"\n")        
     cat("circle area = ", pi * r^2, " = ", sum(pi * r^2), "\ncircle perimenter = ",  2 * pi * r, " = ",  2 * pi * sum(r), "\n")
     grid.polygon(envelopeXY[,1], envelopeXY[,2], gp=gpar(fill="pink", col="transparent", lwd=5), default.units="npc")

Rd file 'tangentLine.Rd':
  \examples lines wider than 100 characters:
                     tangent <- tangentLine(centers[1,], centers[2,], r0, r[2], k=k)  # compute coefficients for the tangent line, if NA, th ... [TRUNCATED]
                             grid.abline(-tangent["c"] / tangent["b"], -tangent["a"] / tangent["b"], gp=gpar(col="blue", lwd=ii), units="npc ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Rd file 'ppoistweedie.Rd':
  \examples lines wider than 100 characters:
     layout.show(1)                                                                                                                          ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Loading this package had a fatal error status code 1
Loading log:
-----------------------------------------------------  psychmeta version 2.3.3  --

Please report any bugs to github.com/psychmeta/psychmeta/issues
or issues@psychmeta.com

We work hard to produce these open-source tools for the R community, 
please cite psychmeta when you use it in your research: 
  Dahlke, J. A., & Wiernik, B. M. (2018). psychmeta: An R package for 
     psychometric meta-analysis. Applied Psychological Measurement. 
     Advance online publication. https://doi.org/10.1177/0146621618795933

Find info about psychmeta on the web at psychmeta.com and twitter.com/psychmetaR
Error: package or namespace load failed for ‘psychmeta’:
 .onAttach failed in attachNamespace() for ‘psychmeta’, details:
  call: open.connection(x, "rb")
  error: HTTP error 404.
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(purrrogress)
  > 
  > test_check("purrrogress")
  ── 1. Failure: R6_txt_progress (@R6_box_progress.R#264)  ───────────────────────
  `pb\$step\(\)` does not match "1000/1000 |=+|\\(100%\\) 00:00:00 remaining\n".
  Actual value: "\\n   1/1000 \|             \|\(0%\) NA remaining"
  
  ── 2. Failure: R6_line_progress (@R6_box_progress.R#358)  ──────────────────────
  pb$bar == paste0("┣", strrep("━", 18), "│") isn't true.
  
  ── 3. Error: R6_line_progress (@R6_box_progress.R#360)  ────────────────────────
  invalid format '% 2d'; use format %f, %e, %g or %a for numeric objects
  Backtrace:
    1. testthat::expect_output(pb$step())
   21. base::sprintf(format, self$current, self$total)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 280 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: R6_txt_progress (@R6_box_progress.R#264) 
  2. Failure: R6_line_progress (@R6_box_progress.R#358) 
  3. Error: R6_line_progress (@R6_box_progress.R#360) 
  
  Error: testthat unit tests failed
  Execution halted
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-patched-gcc/Work/PKGS/R4dfp.Rcheck/00install.out’ for details.
Rd file 'predict.randomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

Rd file 'randomGLM.Rd':
  \usage lines wider than 90 characters:
       # Multi-level classification options - only apply to classification with multi-level response
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, xTest, classify=FALSE, nCandidateCovariates=ncol(xTrain), nBags=10, 

Rd file 'thinRandomGLM.Rd':
  \examples lines wider than 100 characters:
     RGLM = randomGLM(xTrain, yTrain, nCandidateCovariates=ncol(xTrain), nBags=30, keepModels = TRUE, nThreads = 1)

These lines will be truncated in the PDF manual.
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-patched-gcc/Work/PKGS/RArcInfo.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
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-patched-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-patched-gcc/Work/PKGS/re2r.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘GuideToVignettes.Rmd’ using rmarkdown
tlmgr search --file --global '/tikzlibrarytopaths.code.tex'
TLPDB: not a directory, not loading: /home/hornik/lib/texmf/
tlmgr: running in usermode, did you call `tlmgr init-usertree'?
Warning in system2("tlmgr", args, ...) :
  running command ‘'tlmgr' search --file --global '/tikzlibrarytopaths.code.tex'’ had status 2
Warning in parse_packages(logfile, quiet = c(TRUE, FALSE, FALSE)) :
  Failed to find a package that contains tikzlibrarytopaths.code.tex
! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.74 ...enter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

Error: processing vignette 'GuideToVignettes.Rmd' failed with diagnostics:
Failed to compile GuideToVignettes.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See GuideToVignettes.log for more info.
--- failed re-building ‘GuideToVignettes.Rmd’

--- re-building ‘ProgramFlow.Rmd’ using rmarkdown
--- finished re-building ‘ProgramFlow.Rmd’

--- re-building ‘readJDX.Rmd’ using rmarkdown
--- finished re-building ‘readJDX.Rmd’

--- re-building ‘MiniDIFDUP_1.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_1.Rnw’

--- re-building ‘MiniDIFDUP_2.Rnw’ using Sweave
--- finished re-building ‘MiniDIFDUP_2.Rnw’

SUMMARY: processing the following file failed:
  ‘GuideToVignettes.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("rglobi")
  Loading required package: rglobi
  ── 1. Failure: interaction matrix with interaction type can be retrieved (@test-
  unlist(interaction.matrix[[2]]) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 31 | SKIPPED: 2 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: interaction matrix with interaction type can be retrieved (@test-globi.R#113) 
  
  Error: testthat unit tests failed
  Execution halted
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-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:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RMariaDB.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/rncl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Quitting from lines 188-195 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Column `is_oa` is unknown
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
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-patched-gcc/Work/PKGS/rphast.Rcheck/00install.out’ for details.
Note: information on .o files is not available
File ‘/home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/PKGS/rtfbs.Rcheck/00install.out’ for details.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/RVowpalWabbit.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-patched-gcc/Work/PKGS/scio.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-patched-gcc/Work/PKGS/sdwd.Rcheck/00install.out’ for details.
Rd file 'SJ.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     #Fit conditional independence graph at one lambda , using the default basis functions (cubic polynomials).
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

Rd file 'generate.dag.data.Rd':
  \usage lines wider than 90 characters:
     generate.dag.data(g, n, basesd = 1, basemean = 0, bfuns = function(x){cbind(x, x^2, x^3)}, 
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)

Rd file 'spacejam-package.Rd':
  \examples lines wider than 100 characters:
     #with standard deviations of 1, 0.5 and 0.5, (i.e. giving more weight to linear association than quadratic or cubic)
     plot(g, layout=mylayout, edge.color = "gray50", vertex.color = "red", vertex.size = 3, vertex.label = NA, edge.arrow.size = 0.4, main=" ... [TRUNCATED]

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [14s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /home/hornik/tmp/R.check/r-patched-gcc/Work/build/Packages/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/RtmpSvnI4s/file21f86981e407
  ── 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
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-patched-gcc/Work/PKGS/SSN.Rcheck/00install.out’ for details.
Found the following significant warnings:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/subprocess.Rcheck/00install.out’ for details.
Rd file 'SyNet-package.rd':
  \examples lines wider than 100 characters:
       # Run NAM method on the previously inferred sympatry network                                           

Rd file 'acshgral.rd':
  \examples lines wider than 100 characters:
       #Display relationships into a parenthetical notation. You can track the indices of the species in the

Rd file 'gridinfer.rd':
  \examples lines wider than 100 characters:
       #are nested inside it. In a network analysis this kind of element will behave as intermediary node.  

Rd file 'reweight.rd':
  \examples lines wider than 100 characters:
       plot(unlist(ej),unlist(reweight(ej)), xlab = "Input matrix", ylab = "Reweighted matrix", main = "First reweighting")

These lines will be truncated in the PDF manual.
Running ‘testthat.R’ [83s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by RJavaTools to method java.util.ArrayList$Itr.hasNext()
  WARNING: Please consider reporting this to the maintainers of RJavaTools
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  ── 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  ───────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘texPreview-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.kable
> ### Title: Try to coerce an object into a knitr_kable object
> ### Aliases: as.kable
> 
> ### ** Examples
> 
> 
> tex <- '\\begin{tabular}{llr}
+ \\hline
+ \\multicolumn{2}{c}{Item} \\\\
+ \\cline{1-2}
+ Animal    & Description & Price (\\$) \\\\
+ \\hline
+ Gnat      & per gram    & 13.65      \\\\
+ & each        & 0.01       \\\\
+ Gnu       & stuffed     & 92.50      \\\\
+ Emu       & stuffed     & 33.33      \\\\
+ Armadillo & frozen      & 8.99       \\\\
+ \\hline
+ \\end{tabular}'
> 
> ktex <- as.kable(tex)
> 
> class(ktex)
[1] "knitr_kable"
> 
> attributes(ktex)
$class
[1] "knitr_kable"

$format
[1] "latex"

> 
> ktex
\begin{tabular}{llr}
\hline
\multicolumn{2}{c}{Item} \\
\cline{1-2}
Animal    & Description & Price (\$) \\
\hline
Gnat      & per gram    & 13.65      \\
& each        & 0.01       \\
Gnu       & stuffed     & 92.50      \\
Emu       & stuffed     & 33.33      \\
Armadillo & frozen      & 8.99       \\
\hline
\end{tabular}
> 
> # using an input call
> 
> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, keep_pdf,  : 
   
! LaTeX Error: File `/tmp/Rtmp0bn6gd/tex_temp.tex ' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
 
l.17 \input{ /tmp/Rtmp0bn6gd/tex_temp.tex }
 ^^M 
!  ==> Fatal error occurred, no output PDF file produced!
Calls: tex_preview -> tex_preview.character -> tex_preview.default
Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-patched-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-patched-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-patched-gcc/Work/PKGS/text2vec.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10m/11m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(text2vec)
  > library(mlapi)
  > data("movie_review")
  > test_check("text2vec")
  Killed
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-patched-gcc/Work/PKGS/TukeyRegion.Rcheck/00install.out’ for details.
Running examples in ‘UCSCXenaTools-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: fetch
> ### Title: Fetch Data from UCSC Xena Hosts
> ### Aliases: fetch fetch_dense_values fetch_dataset_samples
> ###   fetch_dataset_identifiers has_probeMap
> 
> ### ** Examples
> 
> library(UCSCXenaTools)
> 
> host <- "https://toil.xenahubs.net"
> dataset <- "tcga_RSEM_gene_tpm"
> samples <- c("TCGA-02-0047-01", "TCGA-02-0055-01", "TCGA-02-2483-01", "TCGA-02-2485-01")
> probes <- c("ENSG00000282740.1", "ENSG00000000005.5", "ENSG00000000419.12")
> genes <- c("TP53", "RB1", "PIK3CA")
> 
> # Fetch samples
> fetch_dataset_samples(host, dataset, 2)
[1] "TCGA-19-1787-01" "TCGA-S9-A7J2-01"
> # Fetch identifiers
> # Fetch expression value by probes
> fetch_dense_values(host, dataset, probes, samples, check = FALSE)
                   TCGA-02-0047-01 TCGA-02-0055-01 TCGA-02-2483-01
ENSG00000282740.1           -9.966          -2.826          -9.966
ENSG00000000005.5           -3.171           4.165          -5.574
ENSG00000000419.12           4.675           6.025           5.826
                   TCGA-02-2485-01
ENSG00000282740.1           -9.966
ENSG00000000005.5           -3.171
ENSG00000000419.12           5.177
> # Fetch expression value by gene symbol (if the dataset has probeMap)
> fetch_dense_values(host, dataset, genes, samples, check = FALSE, use_probeMap = TRUE)
-> Checking if the dataset has probeMap...
-> Done. ProbeMap is found.
Error in UCSCXenaTools:::.xena_post(host, UCSCXenaTools:::.call(xquery,  : 
  Internal Server Error (HTTP 500).
Calls: fetch_dense_values ... .p_dataset_gene_probe_avg -> <Anonymous> -> stop_for_status
Execution halted
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-patched-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-patched-gcc/Work/PKGS/WhopGenome.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [14s/14s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wilson)
  
  Attaching package: 'wilson'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("wilson")
  ── 1. Error: complexHeatmap is downloadable (@test-download.R#38)  ─────────────
  getter call used outside of a complex assignment.
  Backtrace:
    1. testthat::expect_silent(...)
    9. wilson:::download(...)
   11. ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom")
   12. ComplexHeatmap:::.local(object, ...)
   14. ComplexHeatmap::draw(ht_list, ...)
   15. ComplexHeatmap:::.local(object, ...)
   17. ComplexHeatmap::make_layout(...)
   18. ComplexHeatmap:::.local(object, ...)
   20. ComplexHeatmap::make_row_cluster(ht_main)
   21. ComplexHeatmap:::.local(object, ...)
   22. ComplexHeatmap:::make_cluster(object, "row")
   23. base::lapply(dend_list, adjust_dend_by_x)
   24. ComplexHeatmap:::FUN(X[[i]], ...)
   25. ComplexHeatmap:::adj_dend()
   26. ComplexHeatmap:::adj_dend(c(ind, i))
   27. ComplexHeatmap:::adj_dend(c(ind, i))
   30. base::NextMethod("[[")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 55 | SKIPPED: 5 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: complexHeatmap is downloadable (@test-download.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-patched-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning 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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘aaSEA_Documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘aaSEA_Documentation.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R          1.5Mb
    data       2.8Mb
    pictures   2.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R       1.4Mb
    data    1.3Mb
    files   1.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.0Mb
installed size is 21.0Mb
  sub-directories of 1Mb or more:
    data  20.9Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    4.8Mb
    help   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc       2.9Mb
    extdata   1.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘ahn.Rmd’

SUMMARY: processing the following file failed:
  ‘ahn.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘rsvg’
installed size is 12.8Mb
  sub-directories of 1Mb or more:
    extdata  12.1Mb
Running examples in ‘amber-Ex.R’ failed
The error most likely occurred in:

> ### Name: scores.fluxnet.nc
> ### Title: Scores for FLUXNET reference data in NetCDF format
> ### Aliases: scores.fluxnet.nc
> 
> ### ** Examples
> 
> 
> library(amber)
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> library(foreach)
> library(ncdf4)
> library(parallel)
> library(raster)
Loading required package: sp
> long.name <- 'Gross primary productivity'
> nc.mod <- system.file('extdata/modelRegular', 'gpp_monthly.nc', package = 'amber')
> nc.ref <- system.file('extdata/referenceRegular', 'gpp_FLUXNET.nc', package = 'amber')
> mod.id <- 'CLASSIC' # define a model experiment ID
> ref.id <- 'FLUXNET' # give reference dataset a name
> unit.conv.mod <- 86400*1000 # optional unit conversion for model data
> unit.conv.ref <- 86400*1000 # optional unit conversion for reference data
> variable.unit <- 'gC m$^{-2}$ day$^{-1}$' # unit after conversion (LaTeX notation)
> score.weights <- c(1,2,1,1,1) # score weights of S_bias, S_rmse, S_phase, S_iav, S_dist
> # global plot
> scores.fluxnet.nc(long.name, nc.mod, nc.ref, mod.id, ref.id, unit.conv.mod,
+  unit.conv.ref, variable.unit, score.weights)
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(nc.ref) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/amber/extdata/referenceRegular/gpp_FLUXNET.nc
Calls: scores.fluxnet.nc -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning 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 49-64 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.4Mb
Package suggested but not available for checking: ‘ssh’
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   2.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    testdata   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning 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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [105s/119s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(antaresViz)
  Loading required package: antaresRead
  Loading required package: antaresProcessing
  
  Attaching package: 'antaresProcessing'
  
  The following object is masked from 'package:testthat':
  
      compare
  
  Loading required package: spMaps
  Loading required package: sp
  Loading required package: raster
  
  Attaching package: 'raster'
  
  The following object is masked from 'package:antaresProcessing':
  
      getValues
  
  Loading required package: rgeos
  rgeos version: 0.5-2, (SVN revision 621)
   GEOS runtime version: 3.6.3-CAPI-1.10.3 
   Linking to sp version: 1.3-2 
   Polygon checking: TRUE 
  
  > 
  > test_check("antaresViz")
  ── 1. Error: (unknown) (@test-h5Request.R#3)  ──────────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
   1. testthat::describe(...)
   2. [ base::eval(...) ] with 1 more call
   6. antaresRead::writeAntaresH5(pathtemp, overwrite = TRUE)
   7. antaresRead::.writeAntaresH5Fun(...)
   8. rhdf5::h5createFile(path)
   9. rhdf5::H5Fcreate(file)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 264 | SKIPPED: 4 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test-h5Request.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘sdols’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘kebabs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘apcluster.Rnw’ using knitr

Attaching package: 'apcluster'

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

    heatmap

Quitting from lines 387-408 (apcluster.Rnw) 
Error: processing vignette 'apcluster.Rnw' failed with diagnostics:
object 'apres2c' not found
--- failed re-building ‘apcluster.Rnw’

SUMMARY: processing the following file failed:
  ‘apcluster.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘labs.Rmd’ using rmarkdown
Warning 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 32-34 (labs.Rmd) 
Error: processing vignette 'labs.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘labs.Rmd’

--- re-building ‘lines.Rmd’ using rmarkdown
Warning 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 39-40 (lines.Rmd) 
Error: processing vignette 'lines.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘lines.Rmd’

--- re-building ‘starting-with-apexcharts.Rmd’ using rmarkdown
Warning 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 36-40 (starting-with-apexcharts.Rmd) 
Error: processing vignette 'starting-with-apexcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘starting-with-apexcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘labs.Rmd’ ‘lines.Rmd’ ‘starting-with-apexcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   3.3Mb
Package suggested but not available for checking: ‘qCBA’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    fontawesome-5.3.1   2.8Mb
    help                1.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    help   1.1Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data      1.1Mb
    extdata   3.8Mb
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("arulesCBA")
  Loading required package: Matrix
  Loading required package: arules
  
  Attaching package: 'arules'
  
  The following objects are masked from 'package:base':
  
      abbreviate, write
  
  Loading required package: discretization
  Loading required package: glmnet
  Loaded glmnet 3.0-1
  
  > 
  > test_check("arulesCBA")
  Apriori
  
  Parameter specification:
   confidence minval smax arem  aval originalSupport maxtime support minlen
          0.8    0.1    1 none FALSE            TRUE       5    0.01      1
   maxlen target   ext
       10  rules FALSE
  
  Algorithmic control:
   filter tree heap memopt load sort verbose
      0.1 TRUE TRUE  FALSE TRUE    2    TRUE
  
  Absolute minimum support count: 1 
  
  set item appearances ...[14 item(s)] done [0.00s].
  set transactions ...[14 item(s), 120 transaction(s)] done [0.00s].
  sorting and recoding items ... [14 item(s)] done [0.00s].
  creating transaction tree ... done [0.00s].
  checking subsets of size 1 2 3 4 5 done [0.00s].
  writing ... [76 rule(s)] done [0.00s].
  creating S4 object  ... done [0.00s].
  ── 1. Failure: (unknown) (@test-RCAR.R#7)  ─────────────────────────────────────
  length(rules(rcar_classifier)) not equal to 20L.
  1/1 mismatches
  [1] 21 - 20 == 1
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-RCAR.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘REBayes’
Error(s) in re-building vignettes:
  ...
--- re-building ‘asmapvignette.Rnw’ using knitr
Warning in summary.cross(cross) :
  Some markers at the same position on chr 1B1,1D,2B,2D1,3A,3B,3D,4A,5A,5B,5D,6D,7A,7B,7D; use jittermap().
Warning in summary.cross(cross) :
  Some chromosomes > 1000 cM in length; there may be a problem with the genetic map.
  (Perhaps it is in basepairs?)
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7,L.8,L.9; use jittermap().
Warning in heatMap(mapBC6, chr = c("L.3", "L.5", "L.8", "L.9"), lmax = 70) :
  Running est.rf.
Warning in summary.cross(cross) :
  Some markers at the same position on chr L.1,L.2,L.3,L.4,L.5,L.6,L.7; use jittermap().
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc        2.4Mb
    full_doc   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 57-76 (Data_Analysis_with_augmentedRCBD.Rmd) 
Error: processing vignette 'Data_Analysis_with_augmentedRCBD.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Data_Analysis_with_augmentedRCBD.Rmd’

SUMMARY: processing the following file failed:
  ‘Data_Analysis_with_augmentedRCBD.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 73.8Mb
  sub-directories of 1Mb or more:
    java  73.8Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.4Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    data   1.1Mb
    doc    2.0Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.1Mb
Running ‘testthat.R’ [34s/41s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(BAS)
  > 
  > test_check("BAS")
  ── 1. Failure: herdity and BAS (@test-bas-glm.R#420)  ──────────────────────────
  pima_BAS$probne0 not equal to pima_BAS_no$probne0.
  6/7 mismatches (average diff: 0.0696)
  [2] 0.11013 - 0.1136 == -3.47e-03
  [3] 1.00000 - 1.0000 == -2.54e-06
  [4] 0.63062 - 0.8284 == -1.98e-01
  [5] 0.02193 - 0.0220 == -1.03e-04
  [6] 0.00771 - 0.0101 == -2.42e-03
  [7] 0.31878 - 0.1051 ==  2.14e-01
  
  
   Marginal Posterior Summaries of Coefficients: 
  
   Using  BMA 
  
   Based on the top  16 models 
             post mean  post SD   post p(B != 0)
  Intercept  95.42308    0.67885   1.00000      
  X1          1.40116    0.35351   0.97454      
  X2          0.42326    0.38407   0.76017      
  X3         -0.03997    0.33398   0.30660      
  X4         -0.22077    0.36931   0.44354      
  
  Call:
  bas.lm(formula = Y ~ ., data = Hald, prior = "BIC", modelprior = uniform())
  
  
   Marginal Posterior Inclusion Probabilities: 
  Intercept         X1         X2         X3         X4  
     1.0000     0.9856     0.7921     0.4705     0.5220  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 150 | SKIPPED: 0 | WARNINGS: 105 | FAILED: 1 ]
  1. Failure: herdity and BAS (@test-bas-glm.R#420) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    3.0Mb
    libs   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   4.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    help   1.5Mb
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.3Mb
Running ‘testthat.R’ [24s/26s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bcgam)
  Loading required package: nimble
  nimble version 0.8.0 is loaded.
  For more information on NIMBLE and a User Manual,
  please visit http://R-nimble.org.
  
  Attaching package: 'nimble'
  
  The following object is masked from 'package:stats':
  
      simulate
  
  > 
  > test_check("bcgam")
  thin = 1: tau, betalpha, sigma, eta
  ── 1. Error: (unknown) (@testthat.R#3)  ────────────────────────────────────────
  Failed to create the shared library.
  Backtrace:
   1. bcgam::bcgam(...)
   2. bcgam:::bcgam.fit(...)
   3. nimble::compileNimble(gaus)
   4. project$compileModel(units[[i]], control = control, showCompilerOutput = showCompilerOutput)
   5. cppProj$compileFile(compileList, showCompilerOutput)
   6. nimble:::compileDynamicRegistrations(showCompilerOutput = showCompilerOutput)
   7. nimble:::compileStaticCode(dllName, cppName, showCompilerOutput)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@testthat.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Bclim.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
Warning in predictExtrapUp(alpha, lambda, beta, predictPositionsRescaled[depthIndRange],  :
  Unable to find suitable chronologies for top of core - truncated to date of extraction
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    doc    2.7Mb
Package suggested but not available for checking: ‘BRugs’
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘lumi’
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

--- re-building ‘abcd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/BFpack.Rcheck/00install.out’ for details.
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    include  145.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.9Mb
Running examples in ‘bigdist-Ex.R’ failed
The error most likely occurred in:

> ### Name: bigdist
> ### Title: Read or Create a distance matrix on disk
> ### Aliases: bigdist
> 
> ### ** Examples
> 
> # basics of 'bigdist'
> # create a random matrix
> set.seed(1)
> amat <- matrix(rnorm(1e3), ncol = 10)
> td   <- tempdir()
> 
> # create a bigdist object with FBM (file-backed matrix) on disk
> temp <- bigdist(mat = amat, file = file.path(td, "temp_ex1"))
----
Location: /tmp/Rtmpd8a4gN/working_dir/Rtmpsea4rV/temp_ex1_100_float.bk
Size on disk: 0 GB
Computing distances ... 
Completed!
----
> temp
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp$fbm$backingfile
[1] "/tmp/Rtmpd8a4gN/working_dir/Rtmpsea4rV/temp_ex1_100_float.bk"
> temp$fbm[1, 2]
[1] 4.631341
> 
> # connect to FBM on disk as a bigdist object
> temp2 <- bigdist(file = file.path(td, "temp_ex1_100_float"))
> temp2
$fbm
A Filebacked Big Matrix of type 'float' with 100 rows and 100 columns.

attr(,"class")
[1] "bigdist"
> temp2$fbm[1,2]

 *** caught segfault ***
address fd100190, cause 'invalid permissions'

Traceback:
 1: extractMat(x$address, i, j)
 2: extract_matrix(x, transform_ind(i, n), transform_ind(j, m))
 3: temp2$fbm[1, 2]
 4: temp2$fbm[1, 2]
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning in engine$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]="webshot333b24a92a1f.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot333b24a92a1f.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

SUMMARY: processing the following file failed:
  ‘analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   2.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘billboarder-intro.Rmd’ using rmarkdown
Warning 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 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-intro.Rmd’

--- re-building ‘billboarder-mapping.Rmd’ using rmarkdown
Warning 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 44-46 (billboarder-mapping.Rmd) 
Error: processing vignette 'billboarder-mapping.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-mapping.Rmd’

--- re-building ‘billboarder-options.Rmd’ using rmarkdown
Warning 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 26-29 (billboarder-options.Rmd) 
Error: processing vignette 'billboarder-options.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder-options.Rmd’

--- re-building ‘billboarder.Rmd’ using rmarkdown
Warning 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 37-56 (billboarder.Rmd) 
Error: processing vignette 'billboarder.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘billboarder.Rmd’

SUMMARY: processing the following files failed:
  ‘billboarder-intro.Rmd’ ‘billboarder-mapping.Rmd’
  ‘billboarder-options.Rmd’ ‘billboarder.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘csaw’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘BioCircos.Rmd’

SUMMARY: processing the following file failed:
  ‘BioCircos.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.7Mb
    extdata   7.8Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data      1.6Mb
    extdata   2.7Mb
Running examples in ‘bioRad-Ex.R’ failed
The error most likely occurred in:

> ### Name: example_scan
> ### Title: Example object of class 'scan'
> ### Aliases: example_scan
> ### Keywords: datasets
> 
> ### ** Examples
> 
> # get summary of example scan:
> summary(example_scan)
                  Polar scan (class scan)

     parameters:  VRADH DBZH ZDR RHOHV PHIDP 
elevation angle:  0.5 deg
           dims:  480 bins x 360 rays
> 
> # example_scan was created with:
> pvolfile <- system.file("extdata", "volume.h5", package = "bioRad")
> pvol <- read_pvolfile(pvolfile)
Error in H5Fopen(file, "H5F_ACC_RDONLY", native = native) : 
  HDF5. File accessibilty. Unable to open file.
Calls: read_pvolfile ... is.odimfile -> h5ls -> h5checktypeOrOpenLoc -> H5Fopen
Execution halted
Running ‘testthat.R’ [14s/18s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(bioRad)
  Welcome to bioRad version 0.4.0
  Warning: no running Docker daemon found Warning: bioRad functionality
  requiring Docker has been disabled
  
  To enable Docker functionality, start Docker and run 'check_docker()'
  in R
  > 
  > test_check("bioRad")
  ── 1. Error: Read a vertical profile (@test-read_vpfiles.R#5)  ─────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_s3_class(readvp(vpfile), "vp")
    4. bioRad::readvp(vpfile)
    5. bioRad::read_vpfiles(...)
    6. bioRad:::read_vp(files)
    7. bioRad::is.vpfile(file)
    8. bioRad::get_odim_object_type(file)
    9. bioRad:::is.odimfile(file)
   10. rhdf5::h5ls(file, recursive = FALSE)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ── 2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13)  ────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. testthat::expect_is(readvp.list(c(vpfile, vpfile)), "list")
    4. bioRad::readvp.list(c(vpfile, vpfile))
    5. bioRad::read_vpfiles(...)
    6. base::lapply(files, read_vp)
    7. bioRad:::FUN(X[[i]], ...)
    8. bioRad::is.vpfile(file)
    9. bioRad::get_odim_object_type(file)
   10. bioRad:::is.odimfile(file)
   11. rhdf5::h5ls(file, recursive = FALSE)
   12. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   13. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 6 | FAILED: 2 ]
  1. Error: Read a vertical profile (@test-read_vpfiles.R#5) 
  2. Error: Read multiple vertical profiles (@test-read_vpfiles.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    help   2.2Mb
Package suggested but not available for checking: ‘Seurat’
Package suggested but not available for checking: ‘IHW’
Running ‘spelling.R’
  Running ‘testthat.R’ [12s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(blastula)
  > 
  > test_check("blastula")
  ── 1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10)  ───────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(rmd_path, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 188 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Invalid maximum heap size: -Xmx4G
The specified size exceeds the maximum representable size.
Namespaces in Imports field not imported from:
  ‘glmnet’ ‘gtools’ ‘knitr’ ‘nnet’ ‘parallel’ ‘rJava’ ‘reshape’
  ‘rmarkdown’ ‘shinyjs’
  All declared Imports should be used.
Missing or unexported object: ‘xgboost::predict’
Running examples in ‘blockcluster-Ex.R’ failed
The error most likely occurred in:

> ### Name: blockcluster
> ### Title: Co-Clustering Package
> ### Aliases: blockcluster
> 
> ### ** Examples
> 
> 
> ## Simple example with simulated binary data
> ## load data
> data(binarydata)
> ## usage of coclusterBinary function in its most simplest form
> out<-coclusterBinary(binarydata,nbcocluster=c(2,3))

 *** caught segfault ***
address c, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘blockcluster_tutorial.Rnw’ using Sweave
Loading required package: rtkore
Loading required package: Rcpp

Attaching package: ‘rtkore’

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

    LdFlags

blockcluster version 4.4.3 loaded

----------------
Copyright (C)  <MODAL team @INRIA,Lille & U.M.R. C.N.R.S. 6599 Heudiasyc, UTC>
Please post questions and bugs at: <https://gforge.inria.fr/forum/forum.php?forum_id=11190&group_id=3679>
Running examples in ‘blockmodeling-Ex.R’ failed
The error most likely occurred in:

> ### Name: REGE
> ### Title: REGE - Algorithms for compiting (dis)similarities in terms of
> ###   regular equivalnece
> ### Aliases: REGE REGE.for REGE.nm.for REGE.ow REGE.ow.for REGE.ownm.for
> ###   REGD.for REGD.ow.for REGE.FC REGE.FC.ow REGD.ne.for REGD.ow.ne.for
> ###   REGE.ne.for REGE.nm.diag.for REGE.nm.ne.for REGE.ow.ne.for
> ###   REGE.ownm.diag.for REGE.ownm.ne.for
> ### Keywords: cluster graphs
> 
> ### ** Examples
> 
> n <- 20
> net <- matrix(NA, ncol = n, nrow = n)
> clu <- rep(1:2, times = c(5, 15))
> tclu <- table(clu)
> net[clu == 1, clu == 1] <- 0
> net[clu == 1, clu == 2] <- rnorm(n = tclu[1] * tclu[2], mean = 4, sd = 1) * sample(c(0, 1),
+    size = tclu[1] * tclu[2], replace = TRUE, prob = c(3/5, 2/5))
> net[clu == 2, clu == 1] <- 0
> net[clu == 2, clu == 2] <- 0
> 
> D <- REGE.for(M = net)$E # Any other REGE function can be used
> plot.mat(net, clu = cutree(hclust(d = as.dist(1 - D), method = "ward"),
+    k = 2))
The "ward" method has been renamed to "ward.D"; note new "ward.D2"
> # REGE returns similarities, which have to be converted to
> # disimilarities
> 
> res <- optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss", blocks = "reg")


Starting optimization of the partiton 1 of 10 partitions.
Starting partition: 1 2 1 1 1 1 1 1 1 2 2 1 2 2 2 2 2 1 1 1 

 *** caught segfault ***
address f7d2544, cause 'memory not mapped'

Traceback:
 1: optParC(M = M, clu = temppar, approaches = approaches, blocks = blocks,     useMulti = useMulti, save.initial.param = save.initial.param.opt,     ...)
 2: optRandomParC(M = net, k = 2, rep = 10, approaches = "hom", homFun = "ss",     blocks = "reg")
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘BoolNet_package_vignette.Snw.Rnw’ using Sweave

Error: processing vignette 'BoolNet_package_vignette.Snw.Rnw' failed with diagnostics:
 chunk 13 
Error in net$interactions[[idx]][[functionIndices[idx]]] : 
  subscript out of bounds

--- failed re-building ‘BoolNet_package_vignette.Snw.Rnw’

SUMMARY: processing the following file failed:
  ‘BoolNet_package_vignette.Snw.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘break_caret.Rmd’ using rmarkdown
Warning 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: lattice
Loading required package: ggplot2
--- finished re-building ‘break_caret.Rmd’

--- re-building ‘break_glm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_glm.Rmd’

--- re-building ‘break_lm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_lm.Rmd’

--- re-building ‘break_randomForest.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_randomForest.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘break_ranger.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- re-building ‘break_svm.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_svm.Rmd’

--- re-building ‘break_xgboost.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘break_xgboost.Rmd’

SUMMARY: processing the following file failed:
  ‘break_ranger.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R     3.3Mb
    doc   2.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bin    3.1Mb
    doc    1.3Mb
    libs   3.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    AdminLTE3-3.0.0   1.1Mb
    doc               2.2Mb
    help              1.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘simple_plotting.Rmd’ using rmarkdown
Warning 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: Removed 4550 rows containing missing values (geom_path).
Quitting from lines 173-174 (simple_plotting.Rmd) 
Error: processing vignette 'simple_plotting.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘simple_plotting.Rmd’

SUMMARY: processing the following file failed:
  ‘simple_plotting.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘examples.Rmd’ using rmarkdown
Warning 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


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]="webshot229413ae210e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot229413ae210e.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
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package which this enhances but not available for checking: ‘FastRWeb’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Task-queue-with-callr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-23 (Task-queue-with-callr.Rmd) 
Error: processing vignette 'Task-queue-with-callr.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Task-queue-with-callr.Rmd’

SUMMARY: processing the following file failed:
  ‘Task-queue-with-callr.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R        1.3Mb
    data     1.8Mb
    models   2.5Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning 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 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘cartograflow.Rmd’

SUMMARY: processing the following file failed:
  ‘cartograflow.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    extdata   6.2Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    extdata   9.8Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    doc    1.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
Package suggested but not available for checking: ‘iptools’
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   2.5Mb
Running examples in ‘ChocoLattes-Ex.R’ failed
The error most likely occurred in:

> ### Name: make_productions_page
> ### Title: Generate HTML page with productions list and summary chart
> ### Aliases: make_productions_page
> 
> ### ** Examples
> 
> 
> # Load example data and convert it to a lattes list
> CV.dir <- system.file("extdata", package="ChocoLattes")
> 
> # Define the aliases of authors "Felipe Campelo" and "Lucas S. Batista":
> # (all aliases will be converted to the first name provided for each author)
> my.aliases <- list(c("Felipe Campelo",
+                      "Felipe Campelo Franca Pinto",
+                      "Felipe Campelo F. Pinto",
+                      "F.C.F. Pinto"),
+                    c("Lucas S. Batista",
+                      "Lucas Batista",
+                      "Lucas de Souza Batista",
+                      "Lucas Souza Batista"))
> 
> lattes.list <- lattes_to_list(CV.dir         = CV.dir,
+                               author.aliases = my.aliases)
> 
> 
> # Build productions page:
> make_productions_page(lattes.list,
+                       chart.type     = "ggplot2",
+                       h1.title       = "ORCS Lab",
+                       h2.title       = "UFMG, Brazil",
+                       language       = "EN")
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    doc    1.7Mb
    help   2.3Mb
Running ‘testthat.R’ [52s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(circumplex)
  > 
  > test_check("circumplex")
  ── 1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17)  ─
  `qb` not equivalent to as_radian(as_degree(c(180, 225, 270, 315, 0))).
  1/5 mismatches
  [5] 6.28 - 0 == 6.28
  
  ── 2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27)  ─
  `qb` not equivalent to as_radian(as_degree(c(270, 315, 0, 45, 90))).
  1/5 mismatches
  [3] 6.28 - 0 == 6.28
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 204 | SKIPPED: 6 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#17) 
  2. Failure: Quantile for circular radians works (@test-ssm_bootstrap.R#27) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘rggobi’
Running ‘testthat.R’ [33s/43s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(classiFunc)
  > 
  > test_check("classiFunc")
  ── 1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100)
  all(as.vector(dist1) <= as.vector(dist3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 54 | SKIPPED: 0 | WARNINGS: 780 | FAILED: 1 ]
  1. Failure: computeDistMat works rucrdtw metrics (@test_computeDistMat.R#100) 
  
  Error: testthat unit tests failed
  Execution halted
Package which this enhances but not available for checking: ‘RWeka’
Error(s) in re-building vignettes:
  ...
--- re-building ‘the_clusterR_package.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 404-417 (the_clusterR_package.Rmd) 
Error: processing vignette 'the_clusterR_package.Rmd' failed with diagnostics:
std::bad_alloc
--- failed re-building ‘the_clusterR_package.Rmd’

SUMMARY: processing the following file failed:
  ‘the_clusterR_package.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cmpprocess-Ex.R’ failed
The error most likely occurred in:

> ### Name: cmpproc
> ### Title: COM Poisson Process Parameter Estimation.
> ### Aliases: cmpproc
> 
> ### ** Examples
> 
> ## Standard usage
> data(floodcount)
> cmpproc(floodcount$Counts)
Error in solve.default(H) : 
  system is computationally singular: reciprocal condition number = 0
Calls: cmpproc -> single.cmp -> diag -> solve -> solve.default
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.1Mb
    extdata   1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Running-CoDiNA.Rmd’ using rmarkdown
Warning in engine$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 100-105 (Running-CoDiNA.Rmd) 
Error: processing vignette 'Running-CoDiNA.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘Running-CoDiNA.Rmd’

SUMMARY: processing the following file failed:
  ‘Running-CoDiNA.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [128s/166s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(shinytest)
  shinytest requires a headless web browser (PhantomJS) to record and run tests.
  To install it, run shinytest::installDependencies()
  If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
  > library(colocr)
  > 
  > test_check("colocr")
  ── 1. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#3
  all.equal(...) isn't true.
  
  ── 2. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#3
  all.equal(...) isn't true.
  
  ── 3. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$pcc, 3), round(unlist(corr), 3)) isn't true.
  
  ── 4. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$moc, 3), round(unlist(corr), 3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 38 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#32) 
  2. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#35) 
  3. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#126) 
  4. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.3Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
Package suggested but not available for checking: ‘rscala’
Error(s) in re-building vignettes:
  ...
--- re-building ‘commonsMath.Rmd’ using rmarkdown
Warning 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 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
there is no package called 'rscala'
--- failed re-building ‘commonsMath.Rmd’

SUMMARY: processing the following file failed:
  ‘commonsMath.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc   2.3Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data      6.5Mb
    extdata   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chamber.Rmd’ using rmarkdown
Warning 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 32-33 (chamber.Rmd) 
Error: processing vignette 'chamber.Rmd' failed with diagnostics:
HTTP error 500
--- failed re-building ‘chamber.Rmd’

--- re-building ‘senate.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

--- finished re-building ‘senate.Rmd’

SUMMARY: processing the following file failed:
  ‘chamber.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘cooccurNet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coocnet
> ### Title: coocnet
> ### Aliases: coocnet
> 
> ### ** Examples
> 
> cooccurNetwork  = coocnet(dataFile=getexample(dataType="protein"), dataType="protein")
reading file......
completed. (10,329)
preprocess file......Error in if (pred >= memsize * alpha || ncol > 150 || (nrow > 30000 &  : 
  missing value where TRUE/FALSE needed
Calls: coocnet ... cooccur.dataprepreprocess.preprocess -> inmemoryflag
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Extending-cooccurNet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 176-178 (Extending-cooccurNet.Rmd) 
Error: processing vignette 'Extending-cooccurNet.Rmd' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building ‘Extending-cooccurNet.Rmd’

SUMMARY: processing the following file failed:
  ‘Extending-cooccurNet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    R     2.4Mb
    doc   6.4Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.8Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_coveffectsplot.Rmd’ using rmarkdown
Warning 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 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction_to_coveffectsplot.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction_to_coveffectsplot.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘SNPRelate’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   8.0Mb
Running examples in ‘Crossover-Ex.R’ failed
The error most likely occurred in:

> ### Name: CrossoverDesign-class
> ### Title: Class CrossoverDesign
> ### Aliases: CrossoverDesign-class CrossoverDesign
> ###   show,CrossoverDesign-method print,CrossoverDesign-method
> ### Keywords: graphs
> 
> ### ** Examples
> 
> 
> 
> design <- t(rbind(c(1,1,2,2),
+                   c(2,2,1,1),
+                   c(1,1,2,2),
+                   c(2,2,1,1),
+                   c(1,2,2,1),
+                   c(2,1,1,2)))
>                    
> new("CrossoverDesign", design)
 (s=6, p=4, v=2)
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    2    1    2    1    2
[2,]    1    2    1    2    2    1
[3,]    2    1    2    1    2    1
[4,]    2    1    2    1    1    2

Error in rcd(design, v = v, model = model) : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: <Anonymous> ... <Anonymous> -> cat -> design.efficiency -> estimable -> rcd
Execution halted
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(Crossover)
  Loading required package: rJava
  Loading required package: CommonJavaJars
  Loading required package: JavaGD
  Loading required package: ggplot2
  > 
  > test_check("Crossover")
  Skipping design tests for v=2.
  ── 1. Error: (unknown) (@test-efficiency.R#217)  ───────────────────────────────
  function 'dataptr' not provided by package 'Rcpp'
  Backtrace:
   1. Crossover:::test.eff()
   2. Crossover::design.efficiency(design)
   3. Crossover:::estimable(design, v, model, C)
   4. Crossover:::rcd(design, v = v, model = model)
Error(s) in re-building vignettes:
  ...
--- re-building ‘Crossover.Rnw’ using knitr
Loading required package: mvtnorm
Loading required package: survival
Loading required package: TH.data

Attaching package: 'TH.data'

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

    geyser

Quitting from lines 243-247 (Crossover.Rnw) 
Error: processing vignette 'Crossover.Rnw' failed with diagnostics:
function 'dataptr' not provided by package 'Rcpp'
--- failed re-building ‘Crossover.Rnw’

SUMMARY: processing the following file failed:
  ‘Crossover.Rnw’

Error: Vignette re-building failed.
Execution halted
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
Re-running with no redirection of stdout/stderr.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   5.1Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/csp.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/ripley/R/packages/tests32/ctsem.Rcheck/00install.out’ for details.
Package required but not available: ‘scs’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘cycling_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘cycling_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    img   4.7Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    Pied_Flycatchers_1   2.5Mb
    Pied_Flycatchers_2   1.3Mb
    doc                  1.2Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    java   7.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    help   2.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Warning 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: whoami:  not found
sh: git:  not found
sh: git:  not found
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).
--- failed re-building ‘extending_dataMaid.Rmd’

SUMMARY: processing the following file failed:
  ‘extending_dataMaid.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘get_started.Rmd’

SUMMARY: processing the following file failed:
  ‘get_started.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   5.7Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs   2.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning 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 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/dbarts.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RPostgres’
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    sample_data   3.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’ using rmarkdown
Warning 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


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:
there is no package called 'webshot'
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

SUMMARY: processing the following file failed:
  ‘MultiObjectiveDecisionAnalysisinR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

--- re-building ‘decoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘sjukhus.Rmd’

SUMMARY: processing the following file failed:
  ‘sjukhus.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
Running ‘test-all.R’ [45s/53s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  ── 1. Failure: extract au (@test-pvclust_extract.R#12)  ────────────────────────
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       5.0Mb
    extdata   2.3Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.0Mb
    help   1.4Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rmosek', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘custom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘custom.Rmd’

--- re-building ‘documentation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘documentation.Rmd’

--- re-building ‘objects.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-58 (objects.Rmd) 
Error: processing vignette 'objects.Rmd' failed with diagnostics:
Timeout was reached: [imgur.com] Resolving timed out after 1000 milliseconds
--- failed re-building ‘objects.Rmd’

--- re-building ‘sessioninfo.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sessioninfo.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tests_and_coverage.Rmd’

SUMMARY: processing the following file failed:
  ‘objects.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘multistage_fundamentals.Rmd’ using rmarkdown
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.
Computing non-mst profile_tables over an mst design, did you mean to use profile_tables_mst?
Warning: Column `item_id` joining character vector and factor, coercing into character vector
Warning: Removed 33 rows containing missing values (geom_point).
Quitting from lines 369-405 (multistage_fundamentals.Rmd) 
Error: processing vignette 'multistage_fundamentals.Rmd' failed with diagnostics:
problem cannot be computed
--- failed re-building ‘multistage_fundamentals.Rmd’

SUMMARY: processing the following file failed:
  ‘multistage_fundamentals.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    doc    1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘DGVM3D.Rmd’ using rmarkdown
Warning 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: rgl
Loading required namespace: rmarkdown
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 230-234 (DGVM3D.Rmd) 
Error: processing vignette 'DGVM3D.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘DGVM3D.Rmd’

SUMMARY: processing the following file failed:
  ‘DGVM3D.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.3Mb
Package unavailable to check Rd xrefs: ‘Seurat’
Running examples in ‘diem-Ex.R’ failed
The error most likely occurred in:

> ### Name: convert_to_seurat
> ### Title: Convert an SCE object to Seurat
> ### Aliases: convert_to_seurat
> 
> ### ** Examples
> 
> mm_seur <- convert_to_seurat(x = mb_small, 
+                              targets = FALSE, 
+                              min.features = 500, 
+                              min.cells = 3, 
+                              project = mb_small@name)
Error: Package "Seurat" needed for convert_to_seurat. Please install.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘diem.Rmd’ using rmarkdown
Warning 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 305-311 (diem.Rmd) 
Error: processing vignette 'diem.Rmd' failed with diagnostics:
Package "Seurat" needed for convert_to_seurat. Please install.
--- failed re-building ‘diem.Rmd’

SUMMARY: processing the following file failed:
  ‘diem.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    doc   9.5Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    doc   6.0Mb
Package suggested but not available for checking: ‘RcppRedis’
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    include  15.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   2.1Mb
Running ‘runit.R’ [18s/28s]
  Running ‘testthat.R’ [18s/27s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > running_on_my_machines <- function() {
  +     sys_info <- Sys.info()
  +     r <- sys_info[["nodename"]] %in% c("h7") &&
  +         sys_info[["effective_user"]] == "qwer" &&
  +         .Platform[["OS.type"]] == "unix"
  +     return(r)
  + }
  > 
  > set_NOT_CRAN  <- function() {
  +     is_unset <- is.na(Sys.getenv("NOT_CRAN", unset = NA))
  +     if (running_on_my_machines() && is_unset)
  +         Sys.setenv("NOT_CRAN" = TRUE)
  + }
  > 
  > set_NOT_CRAN()
  > library("testthat")
  > library("document")
  > test_check("document")
  ── R CMD build ─────────────────────────────────────────────────────────────────
  * checking for file ‘.../DESCRIPTION’ ... OK
  * preparing ‘mini.mal’:
  * checking DESCRIPTION meta-information ... OK
  * checking for LF line-endings in source and make files and shell scripts
  * checking for empty or unneeded directories
  * building ‘mini.mal_2.0.0.tar.gz’
  
  ── 1. Error: (unknown) (@test_basic.R#13)  ─────────────────────────────────────
  Still alive
  Backtrace:
   1. document::document(file_name, check_package = TRUE, runit = TRUE)
   2. document:::check_package(...)
   3. rcmdcheck::rcmdcheck(...)
   4. rcmdcheck:::build_package(...)
   7. proc$get_built_file()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test_basic.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Packages which this enhances but not available for checking:
  'gurobi', 'Rmosek'
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    DRomics-shiny   1.8Mb
    extdata         3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-25
Package created on 2019-08-05

Loading required package: nloptr
Loading required package: nloptr
Loading required package: quadprog
Loading required namespace: earth
Loading required package: quadprog
Loading required namespace: earth
Loading required package: future
Quitting from lines 1049-1062 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
--- failed re-building ‘using_drtmle.Rmd’

SUMMARY: processing the following file failed:
  ‘using_drtmle.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
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]="webshot556b63736407.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot556b63736407.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
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    appinformation   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘dsa-vignette.Rmd’ using rmarkdown
Warning 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 37-38 (dsa-vignette.Rmd) 
Error: processing vignette 'dsa-vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘dsa-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘dsa-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
    doc    1.8Mb
    libs   2.3Mb
Package suggested but not available for checking: ‘uwot’
Package unavailable to check Rd xrefs: ‘uwot’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    doc    1.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.4Mb
Running examples in ‘EasyMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: EasyMx-package
> ### Title: EasyMx: Easy modeling in OpenMx
> ### Aliases: EasyMx-package EasyMx
> 
> ### ** Examples
> 
> 
> # Make and run a one factor model
> require(EasyMx)
> 
> data(demoOneFactor)
> fmod <- list(G=names(demoOneFactor))
> fit1 <- emxFactorModel(fmod, demoOneFactor, run=TRUE)
Running Model with 15 parameters
Error: C stack usage  203986068 is too close to the limit
Error: The job for model 'Model' exited abnormally with the error message: User interrupt
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    hac    4.3Mb
Running examples in ‘eDMA-Ex.R’ failed
The error most likely occurred in:

> ### Name: BacktestDMA
> ### Title: Backtest measures for Dynamic Model Averaging and comparison
> ###   with Dynamic Model Selection
> ### Aliases: BacktestDMA
> 
> ### ** Examples
> 
> 
> library(eDMA)
> 
> ## load data
> data("USData")
> 
> ## do DMA, keep the first three predictors fixed and the intercept
> Fit <- DMA(GDPDEF ~ Lag(GDPDEF, 1) + Lag(GDPDEF, 2) + Lag(GDPDEF, 3) +
+             Lag(ROUTP, 1) + Lag(UNEMP, 1), data = USData, vDelta = c(0.9, 0.95, 0.99),
+             vKeep = c(1, 2, 3))

error: sort(): detected NaN
Error in funcEstimate_Eff_par(vY, mF, vDelta, dAlpha, vKeep, dBeta, bZellnerPrior,  : 
  sort(): detected NaN
Calls: DMA -> funcEstimate_Eff_par
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.8Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc       5.3Mb
    extdata   5.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘EHRtemporalVariability.Rmd’

SUMMARY: processing the following file failed:
  ‘EHRtemporalVariability.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    examples   4.2Mb
Package required but not available: ‘uwot’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘spelling.R’
  Running ‘testthat.R’ [33s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(EML)
  > 
  > test_check("EML")
  sh: +RTS:  not found
  ── 1. Error: set_method with additional input files (@test-additional-tests.R#43
  pandoc document conversion failed with error 127
  Backtrace:
   1. EML::set_methods(...)
   2. EML::set_TextType(sampling_file)
   3. EML:::to_docbook(file)
   4. rmarkdown::pandoc_convert(...)
  
  ══  1 queries  ═══════════════
  ✔  Found:  Macrocystis pyrifera
  ══  Results  ═════════════════
  
  ● Total: 1 
  ● Found: 1 
  ● Not Found: 0
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 83 | SKIPPED: 6 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: set_method with additional input files (@test-additional-tests.R#43) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    emoji_fonts   6.6Mb
Running examples in ‘eNetXplorer-Ex.R’ failed
The error most likely occurred in:

> ### Name: plotContingency
> ### Title: generates plot of response vs out-of-bag predictions across
> ###   classes
> ### Aliases: plotContingency
> 
> ### ** Examples
> 
> ## Don't show: 
> set.seed(123)
> fit = eNetXplorer(x=matrix(rnorm(120),ncol=4),y=c(rep(0,15),rep(1,15)),
+ family="binomial",n_run=5, n_perm_null=4,alpha=c(0.5,1))
Error during execution of alpha =  0.5 
> plot(x=fit,plot.type="contingency")
Error in if (x$family %in% c("binomial", "multinomial")) { : 
  argument is of length zero
Calls: plot -> plot.eNetXplorer
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    doc    3.4Mb
    help   3.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning in engine$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 150-151 (epicontacts.Rmd) 
Error: processing vignette 'epicontacts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epicontacts_class.Rmd’

SUMMARY: processing the following file failed:
  ‘epicontacts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘EpiSignalDetection-Ex.R’ failed
The error most likely occurred in:

> ### Name: runEpiSDReport
> ### Title: Run the EpiSignalDetection report (HTML markdown)
> ### Aliases: runEpiSDReport
> 
> ### ** Examples
> 
> #---> OR
> 
> #-- First setting the parameters to run the report for
> input <- list(
+ disease = "Salmonellosis",
+ country = "Portugal",
+ indicator = "Reported cases",
+ stratification = "Confirmed cases",
+ unit = "Month",
+ daterange = c("2011-01-01", "2016-12-31"),
+ algo = "FarringtonFlexible",
+ testingperiod = 6
+ )
> 
> #-- Second running the report based on the EpiSignalDetection::SignalData dataset
> #-- and store it in a temporary folder
> runEpiSDReport(input = input)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running examples in ‘erhcv-Ex.R’ failed
The error most likely occurred in:

> ### Name: VerifyTree
> ### Title: Verify tree structure
> ### Aliases: VerifyTree
> 
> ### ** Examples
> 
> require(HAC)
Loading required package: HAC
Loading required package: copula
> str <- hac(type = 1, tree = list(list(list("X4", "X5", 6),
+                                       "X6", 3), "X1", list("X2", "X3", 10), 1))
> 
> set.seed(2018)
> U.. <- rHAC(1000, str)
Warning in hac2nacopula(hac) : NAs introduced by coercion
[1] "X4 <-> 1"
[1] "X5 <-> 2"
[1] "X6 <-> 3"
[1] "X1 <-> 4"
[1] "X2 <-> 5"
[1] "X3 <-> 6"
> U.. <- U..[,c(4, 5, 6, 1, 2, 3)]
> 
> ## Tree via hclust
> spear <- cor(U.., method = "sp")
> clust <- hclust(dist(spear, method = "maximum"),
+                 method = "complete")
> tree1 <- hclust2tree(clust)
> 
> ## Tree after verification
> tree2 <- VerifyTree(U.., alpha = 0.95,
+                     distance.method = "maximum",
+                     hclust.method = "complete")$Tree
> 
> ## Comparison
> par(mfrow = c(1, 3))
> tree2plot(tree1)
Error in plot.Node(e1$O) : 
  Package "DiagrammeR" is required to plot a `data.tree::Node`object. Please install it.
Calls: tree2plot -> plot -> plot.Node
Execution halted
Running ‘sleep.R’
  Comparing ‘sleep.Rout’ to ‘sleep.Rout.save’ ... OK
  Running ‘testthat.R’ [80s/96s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(estimatr)
  > 
  > test_check("estimatr")
  ── 1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682)  ──
  tidy(rfo)[rfo$term == "X", ] not equivalent to tidy(ro)[ro$term == "X", ].
  Component "std.error": 'is.NA' value mismatch: 1 in current 0 in target
  Component "statistic": 'is.NA' value mismatch: 1 in current 0 in target
  Component "p.value": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.low": 'is.NA' value mismatch: 1 in current 0 in target
  Component "conf.high": 'is.NA' value mismatch: 1 in current 0 in target
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1326 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Handle perfect fits appropriately (@test-lm-robust-fes.R#682) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.1Mb
installed size is 14.6Mb
  sub-directories of 1Mb or more:
    exiftool  14.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_genExPrior.Rmd’ using rmarkdown
Warning 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 58-59 (using_genExPrior.Rmd) 
Error: processing vignette 'using_genExPrior.Rmd' failed with diagnostics:
Failed to create the shared library.
--- failed re-building ‘using_genExPrior.Rmd’

SUMMARY: processing the following file failed:
  ‘using_genExPrior.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Package suggested but not available for checking: ‘RWeka’
Package unavailable to check Rd xrefs: ‘RWeka’
Running ‘run-all.R’
Running the tests in ‘tests/run-all.R’ failed.
Complete output:
  > library(testthat)
  > test_check("farff")
  Loading required package: farff
  ── 1. Error: quick test with small arffs (@test_quick.R#6)  ────────────────────
  there is no package called 'RWeka'
  Backtrace:
   1. farff:::compareRWeka(INST_ARFF_DIR, "iris.arff", data.reader = dreader)
   2. RWeka::read.arff /home/ripley/R/packages/tests32/farff.Rcheck/tests/helper.R:17:2
   3. base::getExportedValue(pkg, name)
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 8 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quick test with small arffs (@test_quick.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
Package suggested but not available for checking: ‘Rserve’
Installation failed.
See ‘/home/ripley/R/packages/tests32/FastRWeb.Rcheck/00install.out’ for details.
Running ‘tinytest.R’
Running the tests in ‘tests/tinytest.R’ failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   home <- length(unclass(packageVersion("fastshap"))[[1L]]) == 4
  +   tinytest::test_package("fastshap", at_home = home)
  + }
  Loading required package: Formula
  Loading required package: plotmo
  Loading required package: plotrix
  Loading required package: TeachingDemos
  
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    Error in fastshap:::genOMat(num_rows, num_cols) : 
    function 'enterRNGScope' not provided by package 'Rcpp'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.5Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(felp)
  
  Attaching package: 'felp'
  
  The following object is masked from 'package:utils':
  
      ?
  
  > 
  > test_check("felp")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   5.1Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Package required but not available: ‘CVXR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning 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 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘quick_charts.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_charts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘selectIndicatorsRedRed.Rmd’

SUMMARY: processing the following file failed:
  ‘lifeExpectancy.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   4.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   3.2Mb
Package suggested but not available for checking: ‘multipanelfigure’
Running examples in ‘float-Ex.R’ failed
The error most likely occurred in:

> ### Name: eigen
> ### Title: eigen
> ### Aliases: eigen eigen,float32-method
> 
> ### ** Examples
> 
> library(float)
> 
> s = flrunif(10, 3)
> cp = crossprod(s)
> 
> eigen(cp)
Found the following significant warnings:
  Warning: namespace ‘rrcov’ is not available and has been replaced
  Warning: namespace ‘robustbase’ is not available and has been replaced
See ‘/home/ripley/R/packages/tests32/flowDiv.Rcheck/00install.out’ for details.
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    fonts   6.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    fonts   7.6Mb
Running ‘testthat.R’ [209s/208s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  ── 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  ──────────────
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 896-920 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
could not find function "doColorRamp"
--- failed re-building ‘Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pcl-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-49 (pcl-vignette.Rmd) 
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘pcl-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘pcl-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘formattable-data-frame.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning 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 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rsocp', 'Rnlminb2', 'Rdonlp2', 'Rsymphony'
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    help   1.6Mb
    libs   5.2Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R   5.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   4.9Mb
    doc    2.1Mb
Package unavailable to check Rd xrefs: ‘RMark’
Packages suggested but not available for checking: 'RWeka', 'FSelector'
Package unavailable to check Rd xrefs: ‘FSelector’
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    data  16.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘chart_themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.4Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   1.7Mb
    libs      2.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gcbd.Rnw’ using Sweave
Warning in packageDescription("gputools") :
  no package 'gputools' was found
Error: processing vignette 'gcbd.Rnw' failed with diagnostics:
at gcbd.Rnw:860, subscript out of bounds
--- failed re-building ‘gcbd.Rnw’

SUMMARY: processing the following file failed:
  ‘gcbd.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    L8NY18   2.1Mb
    doc      1.0Mb
    libs     2.3Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R  10.3Mb
Package suggested but not available for checking: ‘reactome.db’
installed size is 27.3Mb
  sub-directories of 1Mb or more:
    data  27.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geosample-vignette.Rnw’ using knitr
Loading required package: sf
Linking to GEOS 3.6.3, GDAL 2.2.4, PROJ 5.2.0
Loading required package: sp
Loading required package: geoR
--------------------------------------------------------------
 Analysis of Geostatistical Data
 For an Introduction to geoR go to http://www.leg.ufpr.br/geoR
 geoR version 1.7-5.2.1 (built on 2016-05-02) is now loaded
--------------------------------------------------------------

Loading required package: maxLik
Loading required package: miscTools

Please cite the 'maxLik' package as:
Henningsen, Arne and Toomet, Ott (2011). maxLik: A package for maximum likelihood estimation in R. Computational Statistics 26(3), 443-458. DOI 10.1007/s00180-010-0217-1.

If you have questions, suggestions, or comments regarding the 'maxLik' package, please use a forum or 'tracker' at maxLik's R-Forge site:
https://r-forge.r-project.org/projects/maxlik/
Loading required package: raster

Attaching package: 'raster'

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

    maxValue

Loading required package: pdist
Loading required package: Matrix
Quitting from lines 476-516 (geosample-vignette.Rnw) 
Error: processing vignette 'geosample-vignette.Rnw' failed with diagnostics:
cannot allocate vector of size 3.0 Gb
--- failed re-building ‘geosample-vignette.Rnw’

SUMMARY: processing the following file failed:
  ‘geosample-vignette.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-60 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    help   1.6Mb
Packages suggested but not available for checking: 'av', 'gifski'
Error(s) in re-building vignettes:
  ...
--- re-building ‘gganimate.Rmd’ using rmarkdown
Warning 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 253-258 (gganimate.Rmd) 
Error: processing vignette 'gganimate.Rmd' failed with diagnostics:
The av package is required to use av_renderer
--- failed re-building ‘gganimate.Rmd’

SUMMARY: processing the following file failed:
  ‘gganimate.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggBubbles.Rmd’ using rmarkdown
Warning 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: knitr
Loading required package: ggplot2
Loading required package: ggBubbles
Quitting from lines 30-40 (ggBubbles.Rmd) 
Error: processing vignette 'ggBubbles.Rmd' failed with diagnostics:
could not find function "CRANpkg"
--- failed re-building ‘ggBubbles.Rmd’

SUMMARY: processing the following file failed:
  ‘ggBubbles.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    help   2.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc         2.8Mb
    tutorials   1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggimage.Rmd’ using rmarkdown
Warning 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 101-103 (ggimage.Rmd) 
Error: processing vignette 'ggimage.Rmd' failed with diagnostics:
there is no package called 'rsvg'
--- failed re-building ‘ggimage.Rmd’

SUMMARY: processing the following file failed:
  ‘ggimage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning 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

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

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
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot1993505f2157.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1993505f2157.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    R     1.1Mb
    doc   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ggplot2-specs.Rmd’

Profiling Timer Expired
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.8Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    extdata   9.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: Matrix
Quitting from lines 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ggseas.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 125-126 (ggseas.Rmd) 
Error: processing vignette 'ggseas.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘ggseas.Rmd’

SUMMARY: processing the following file failed:
  ‘ggseas.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘glmnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot.cv.glmnet
> ### Title: plot the cross-validation curve produced by cv.glmnet
> ### Aliases: plot.cv.glmnet plot.cv.relaxed
> ### Keywords: models regression
> 
> ### ** Examples
> 
> 
> set.seed(1010)
> n = 1000
> p = 100
> nzc = trunc(p/10)
> x = matrix(rnorm(n * p), n, p)
> beta = rnorm(nzc)
> fx = (x[, seq(nzc)] %*% beta)
> eps = rnorm(n) * 5
> y = drop(fx + eps)
> px = exp(fx)
> px = px/(1 + px)
> ly = rbinom(n = length(px), prob = px, size = 1)
> cvob1 = cv.glmnet(x, y)
Error in intI(j, n = x@Dim[2], dn[[2]], give.dn = FALSE) : 
  'NA' indices are not (yet?) supported for sparse Matrices
Calls: cv.glmnet ... NextMethod -> predict.glmnet -> [ -> [ -> subCsp_cols -> intI
Execution halted
Packages required but not available: 'SeqArray', 'SeqVarTools'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    4.3Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    R  27.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Installation failed.
See ‘/home/ripley/R/packages/tests32/gwsem.Rcheck/00install.out’ for details.
installed size is 127.4Mb
  sub-directories of 1Mb or more:
    R       1.0Mb
    java  125.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$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 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘Basic_use.Rmd’

SUMMARY: processing the following file failed:
  ‘Basic_use.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  readstat/readstat_convert.c:18:42: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:89:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
  src/spss/readstat_sav_parse.rl:197:17: warning: passing argument 2 of ‘libiconv’ from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/haven.Rcheck/00install.out’ for details.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc           2.8Mb
    htmlwidgets   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning 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://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hchinamap.Rmd’

SUMMARY: processing the following file failed:
  ‘hchinamap.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘hdf5r-Ex.R’ failed
The error most likely occurred in:

> ### Name: H5A-class
> ### Title: Class for representing HDF5 attributes
> ### Aliases: H5A-class H5A
> 
> ### ** Examples
> 
> fname <- tempfile(fileext = ".h5")
> file <- H5File$new(fname, mode = "a")
Error in H5File.open(filename, mode, file_create_pl, file_access_pl) : 
  HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed
Calls: <Anonymous> -> <Anonymous> -> H5File.open
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdf5r.Rmd’ using rmarkdown
Warning 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 block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 73-77 (hdf5r.Rmd) 
Error: processing vignette 'hdf5r.Rmd' failed with diagnostics:
HDF5-API Errors:
    error #000: H5F.c in H5Fcreate(): line 444: unable to create file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #001: H5Fint.c in H5F__create(): line 1364: unable to open file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #002: H5Fint.c in H5F_open(): line 1615: unable to lock the file
        class: HDF5
        major: File accessibilty
        minor: Unable to open file

    error #003: H5FD.c in H5FD_lock(): line 1640: driver lock request failed
        class: HDF5
        major: Virtual File Layer
        minor: Can't update object

    error #004: H5FDsec2.c in H5FD_sec2_lock(): line 941: unable to lock file, errno = 14, error message = 'Bad address'
        class: HDF5
        major: File accessibilty
        minor: Bad file ID accessed

--- failed re-building ‘hdf5r.Rmd’

SUMMARY: processing the following file failed:
  ‘hdf5r.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hdnom.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

(process:8228): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 10.5'

(process:8228): Pango-WARNING **: font_face status is: no error has occurred

(process:8228): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:8228): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 10.5', text='M'
Quitting from lines 367-379 (hdnom.Rmd) 
Error: processing vignette 'hdnom.Rmd' failed with diagnostics:
NA/NaN/Inf in foreign function call (arg 16)
--- failed re-building ‘hdnom.Rmd’

SUMMARY: processing the following file failed:
  ‘hdnom.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   5.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning 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: plotly
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

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.16.0

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
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘authentication.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘authentication.Rmd’

--- re-building ‘geocoder.Rmd’ using rmarkdown
Warning 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 51-58 (geocoder.Rmd) 
Error: processing vignette 'geocoder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocoder.Rmd’

--- re-building ‘routing.Rmd’ using rmarkdown
Warning 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 40-48 (routing.Rmd) 
Error: processing vignette 'routing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘routing.Rmd’

--- re-building ‘traffic.Rmd’ using rmarkdown
Warning 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 44-52 (traffic.Rmd) 
Error: processing vignette 'traffic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘traffic.Rmd’

--- re-building ‘weather.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 52-59 (weather.Rmd) 
Error: processing vignette 'weather.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘weather.Rmd’

SUMMARY: processing the following files failed:
  ‘geocoder.Rmd’ ‘routing.Rmd’ ‘traffic.Rmd’ ‘weather.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    doc    4.9Mb
    libs   1.8Mb
Running ‘testthat.R’ [92s/115s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(hesim)
  > 
  > test_check("hesim")
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  Error in flexsurvreg(formula = Surv(futime, fustat) ~ age, data = data_i,  : 
    Initial values for parameters 1,2 out of range
  ── 1. Failure: Simulate costs and QALYs (@test-ctstm.R#379)  ───────────────────
  all(costs[category == "drugs", costs] == 0) isn't true.
  
  ── 2. Failure: Simulate costs and QALYs (@test-ctstm.R#381)  ───────────────────
  all(costs$costs == 0) isn't true.
  
  sample = 1
  sample = 2
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 728 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: Simulate costs and QALYs (@test-ctstm.R#379) 
  2. Failure: Simulate costs and QALYs (@test-ctstm.R#381) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc           3.7Mb
    htmlwidgets   4.1Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Found the following significant warnings:
  mapping.cpp:95:58: warning: ISO C++ says that these are ambiguous, even though the worst conversion for the first is better than the worst conversion for the second:
See ‘/home/ripley/R/packages/tests32/hilbertSimilarity.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RProtoBuf’
Package unavailable to check Rd xrefs: ‘RProtoBuf’
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning 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 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hpackedbubble.Rmd’

SUMMARY: processing the following file failed:
  ‘hpackedbubble.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc   4.3Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R     2.0Mb
    doc   2.6Mb
installed size is 13.6Mb
  sub-directories of 1Mb or more:
    R      2.1Mb
    data   8.1Mb
    doc    2.7Mb
Running ‘testthat.R’ [6s/56s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("httr")
  Loading required package: httr
  ── 1. Failure: if request_perform() throws an error, RETRY passes it on (@test-r
  `RETRY(...)` threw an error with unexpected message.
  Expected match: "resolve host"
  Actual message: "Could not resolve: 98d90a2a254647889e2e4c236fb576cd.com (Domain name not found)"
  Backtrace:
   1. testthat::expect_error(...)
   6. httr::RETRY(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 158 | SKIPPED: 2 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: if request_perform() throws an error, RETRY passes it on (@test-retry.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Running examples in ‘IAPWS95-Ex.R’ failed
The error most likely occurred in:

> ### Name: TDh
> ### Title: Temperature, Function of Density and Enthalpy
> ### Aliases: TDh
> 
> ### ** Examples
> 
> D <- 838.025
> h <- 977.181624
> T_Dh <- TDh(D,h)
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning 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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘ibmsunburst.Rmd’

SUMMARY: processing the following file failed:
  ‘ibmsunburst.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘BSgenome.Mmusculus.UCSC.mm10’
Package unavailable to check Rd xrefs: ‘BSgenome.Mmusculus.UCSC.mm10’
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-70 (example.Rmd) 
Quitting from lines 62-70 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
invalid connection
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    data   1.5Mb
    doc    1.0Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   4.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning 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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning 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 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ifa-Ex.R’ failed
The error most likely occurred in:

> ### Name: ifa.bic
> ### Title: A function to compute the BIC
> ### Aliases: ifa.bic
> ### Keywords: multivariate
> 
> ### ** Examples
> 
> data(memory)

 *** caught segfault ***
address 144959bc, cause 'memory not mapped'

Traceback:
 1: sub(".*\\.", "", x)
 2: fileExt(file)
 3: data(memory)
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘ifaTools-Ex.R’ failed
The error most likely occurred in:

> ### Name: univariatePrior
> ### Title: Univariate priors commonly used in IFA models
> ### Aliases: univariatePrior
> 
> ### ** Examples
> 
> model <- univariatePrior("logit-norm", "x1", -1)
> model$priorParam$values[1,1] <- -.6
> model <- mxRun(model)
Running univariatePrior with 1 parameter
Error: C stack usage  229807252 is too close to the limit
Error: The job for model 'univariatePrior' exited abnormally with the error message: User interrupt
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Quitting from lines 1344-1399 (pritikin-schmidt.Rnw) 
Error: processing vignette 'pritikin-schmidt.Rnw' failed with diagnostics:
Fit not achieved
--- failed re-building ‘pritikin-schmidt.Rnw’

SUMMARY: processing the following file failed:
  ‘pritikin-schmidt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   6.5Mb
Package suggested but not available for checking: ‘tesseract’
installed size is 16.8Mb
  sub-directories of 1Mb or more:
    data      1.5Mb
    doc       5.4Mb
    extdata   1.2Mb
    include   2.9Mb
    libs      4.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    help   1.4Mb
Package unavailable to check Rd xrefs: ‘minfi’
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)
Unsupported platform: SunOS 5.10
For this platform, the path to the binary executable of X-13
has to be manually specified. See ?seasonal for details.
No path to the binary executable of X-13 specified.

You can set 'X13_PATH' manually if you intend to use your own
binaries. See ?seasonal for details.

Error in checkX13(fail = TRUE, fullcheck = FALSE, htmlcheck = FALSE) : 
  Process terminated
Calls: INFL.core_tf -> <Anonymous> -> checkX13
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’ [11s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(inplace)
  > 
  > test_check("inplace")
  ── 1. Failure: in-place operators work in common cases (@test-operators.R#80)  ─
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ── 2. Failure: in-place operators work in common cases (@test-sweep.R#49)  ─────
  `X` not identical to `X2`.
  Objects equal but not identical
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 806 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: in-place operators work in common cases (@test-operators.R#80) 
  2. Failure: in-place operators work in common cases (@test-sweep.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’
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)  ────────────────────────────
  HDF5. File accessibilty. Unable to open file.
  Backtrace:
    1. io:::test_read_write_read(f)
    2. io::qread(infile) /home/ripley/R/packages/tests32/io.Rcheck/tests/helper.R:47:8
    4. io:::qread.hdf5(...)
   10. rhdf5::h5ls(file)
   11. rhdf5:::h5checktypeOrOpenLoc(file, readonly = TRUE, native = native)
   12. rhdf5::H5Fopen(file, "H5F_ACC_RDONLY", native = native)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test_read-write-read.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    extdata   7.7Mb
Package suggested but not available for checking: ‘redux’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    dict   5.0Mb
Package suggested but not available for checking: ‘RProtoBuf’
Running examples in ‘joinet-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.joinet
> ### Title: Extract Coefficients
> ### Aliases: coef.joinet
> 
> ### ** Examples
> 
> n <- 50; p <- 100; q <- 3
> X <- matrix(rnorm(n*p),nrow=n,ncol=p)
> Y <- replicate(n=q,expr=rnorm(n=n,mean=rowSums(X[,1:5])))
> object <- joinet(Y=Y,X=X)
Error in approx(lambda, seq(lambda), sfrac) : 
  need at least two non-NA values to interpolate
Calls: joinet ... NextMethod -> predict.glmnet -> lambda.interp -> approx
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(joinet)
  > 
  > testthat::test_check(package="joinet",stop_on_warning=FALSE)
  ── 1. Error: (unknown) (@test.R#24)  ───────────────────────────────────────────
  need at least two non-NA values to interpolate
  Backtrace:
    1. joinet::joinet(...)
    2. glmnet::cv.glmnet(...)
    3. glmnet:::cv.glmnet.raw(...)
    5. glmnet:::buildPredmat.default(...)
    9. glmnet::predict.glmnet(...)
   10. glmnet:::lambda.interp(lambda, s)
   11. stats::approx(lambda, seq(lambda), sfrac)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3 | SKIPPED: 0 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: (unknown) (@test.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘article.Rmd’ using rmarkdown
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.
--- finished re-building ‘article.Rmd’

--- re-building ‘joinet.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 105-106 (joinet.Rmd) 
Error: processing vignette 'joinet.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
--- failed re-building ‘joinet.Rmd’

SUMMARY: processing the following file failed:
  ‘joinet.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    htmlwidgets   5.0Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc   4.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘kgc-fine.Rmd’ using rmarkdown
Warning 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: shiny
Loading required package: shinythemes
Loading required package: plyr
Quitting from lines 37-53 (kgc-fine.Rmd) 
Error: processing vignette 'kgc-fine.Rmd' failed with diagnostics:
cannot allocate vector of size 640.7 Mb
--- failed re-building ‘kgc-fine.Rmd’

--- re-building ‘kgc-vignette.Rmd’ using rmarkdown
Warning 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: shiny
Loading required package: shinythemes
Loading required package: plyr
--- finished re-building ‘kgc-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘kgc-fine.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘gifski’
Error(s) in re-building vignettes:
  ...
--- re-building ‘advanced.Rmd’ using rmarkdown
Warning 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
Loaded glmnet 3.0-1

--- finished re-building ‘advanced.Rmd’

--- re-building ‘fixed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘fixed.Rmd’

--- re-building ‘hiv.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘hiv.Rmd’

Cpu Limit Exceeded - core dumped
--- re-building ‘knockoff.Rmd’ using rmarkdown
Warning 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
Loaded glmnet 3.0-1

SUMMARY: processing the following file failed:
  ‘knockoff.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    java   6.2Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(KRIG)
  > 
  > test_check("KRIG")
  ── 1. Failure: Same result sequencial and parallel code (@test1.R#15)  ─────────
  `kw` not equal to `nw`.
  1/1 mismatches
  [1] 12611 - 6305 == 6305
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Same result sequencial and parallel code (@test1.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘copper_mining_2d.Rmd’

--- re-building ‘ordinary_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ordinary_kriging.Rmd’

--- re-building ‘simple_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘simple_kriging.Rmd’

--- re-building ‘universal_kriging.Rmd’ using rmarkdown
Warning 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: inv_sympd(): given matrix is not symmetric
--- finished re-building ‘universal_kriging.Rmd’

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   8.5Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   3.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    2.6Mb
    help   1.2Mb
Running ‘config.R’
  Running ‘testthat.R’
Running the tests in ‘tests/config.R’ failed.
Complete output:
  > mac_dir <- "~/Documents/Rtest/"
  > win_dir <- "C:/Rtest"
  > linux_dir <- "~/Documents/Rtest"
  > 
  > switch(Sys.info()['sysname'],
  +        "Darwin" = {working_dir <- mac_dir},
  +        "Windows" = {working_dir <- win_dir},
  +        "Linux" = {working_dir <- linux_dir})
  > 
  > rds_file_name <- "./ranListSmall.rds"
  > llo_file_name <- "./ranListSmall.llo"
  > repeat_time <- 20
  > original <- FALSE
  > compress <- TRUE
  > 
  > # rds_file_name <- "./ranListMid.rds"
  > # llo_file_name <- "./ranListMid.llo"
  > # repeat_time <- 20
  > # original <- FALSE
  > # compress <- TRUE
  > 
  > options(list(largeList.report.progress = FALSE))
  > 
  > if (dir.exists(working_dir)) {
  +   setwd(working_dir)
  +   if (file.exists(rds_file_name)) {
  +     library(futile.logger)
  +     ready_to_test <- TRUE
  +   } else {
  +     ready_to_test <- FALSE
  +   }
  + } else {
  +   ready_to_test <- FALSE
  + }
  Error in dir.exists(working_dir) : object 'working_dir' not found
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_lavaanPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.7Mb
    libs   2.3Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    geojson  11.5Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    htmlwidgets   4.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Learning-leaflet.Rmd’ using rmarkdown
Warning 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 49-69 (Learning-leaflet.Rmd) 
Error: processing vignette 'Learning-leaflet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Learning-leaflet.Rmd’

--- re-building ‘generic-demo.Rmd’ using rmarkdown
Warning 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 22-46 (generic-demo.Rmd) 
Error: processing vignette 'generic-demo.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘generic-demo.Rmd’

--- re-building ‘leaflethex.Rmd’ using rmarkdown
Warning 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 41-48 (leaflethex.Rmd) 
Error: processing vignette 'leaflethex.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘leaflethex.Rmd’

SUMMARY: processing the following files failed:
  ‘Learning-leaflet.Rmd’ ‘generic-demo.Rmd’ ‘leaflethex.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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 67-77 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.9Mb
File ‘leaps/libs/leaps.so’:
  Found ‘__f90_esfw’, possibly from ‘print’ (Fortran), ‘write’
    (Fortran)
    Object: ‘leaps.o’
  Found ‘__f90_eslw’, possibly from ‘print’ (Fortran), ‘write’
    (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.
Compilation used the following non-portable flag(s):
  ‘-mt’
Error(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning 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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Understanding_lime.Rmd’

SUMMARY: processing the following file failed:
  ‘Understanding_lime.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   2.3Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R          1.6Mb
    doc        2.8Mb
    testdata   1.8Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/lmSubsets.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rsymphony’
Error(s) in re-building vignettes:
  ...
--- re-building ‘lspline.Rmd’ using rmarkdown
Warning 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 18-23 (lspline.Rmd) 
Error: processing vignette 'lspline.Rmd' failed with diagnostics:
object 'params' not found
--- failed re-building ‘lspline.Rmd’

SUMMARY: processing the following file failed:
  ‘lspline.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘LUCIDus-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘LUCIDus-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘lvmcomp-Ex.R’ failed
The error most likely occurred in:

> ### Name: StEM_mirt
> ### Title: Stochastic EM algorithm for solving multivariate item response
> ###   theory model
> ### Aliases: StEM_mirt
> 
> ### ** Examples
> 
> # run a toy example based on the M2PL model
> 
> # load a simulated dataset
> attach(data_sim_mirt)
> 
> # generate starting values for the algorithm
> A0 <- Q
> d0 <- rep(0, J)
> theta0 <- matrix(rnorm(N*K, 0, 1),N)
> sigma0 <- diag(1, K) 
> 
> # do the confirmatory MIRT analysis
> # to enable multicore processing, set parallel = T
> mirt_res <- StEM_mirt(response, Q, A0, d0, theta0, sigma0)

Step  1	| 
Step  2	| 
Step  3	| 
Step  4	| 
Step  5	| 
Step  6	| 
Step  7	| 
Step  8	| 
Step  9	| 
Step  10	| 
Step  11	| 
Step  12	| 
Step  13	| 
Step  14	| 
Step  15	|
Running examples in ‘lvnet-Ex.R’ failed
The error most likely occurred in:

> ### Name: lvnet
> ### Title: Confirmatory Latent Variable Network Models
> ### Aliases: lvnet
> 
> ### ** Examples
> 
> # Load dataset:
> library("lavaan")
This is lavaan 0.6-5
lavaan is BETA software! Please report any bugs.

Attaching package: ‘lavaan’

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

    vech

> data(HolzingerSwineford1939)
> Data <- HolzingerSwineford1939[,7:15]
> 
> # Measurement model:
> Lambda <- matrix(0, 9, 3)
> Lambda[1:3,1] <- NA
> Lambda[4:6,2] <- NA
> Lambda[7:9,3] <- NA
> 
> # Fit CFA model:
> CFA <- lvnet(Data, lambda = Lambda)
Error: C stack usage  333878420 is too close to the limit
Error: The job for model 'model' exited abnormally with the error message: User interrupt
Execution halted
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    TS_files     6.0Mb
    base_files   6.5Mb
Packages suggested but not available for checking:
  'av', 'rsvg', 'tesseract', 'gifski'
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc   6.8Mb
Packages unavailable to check Rd xrefs: ‘rsvg’, ‘tesseract’, ‘gifski’, ‘av’
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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 library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'rsvg'
Quitting from lines 227-236 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Magick: non-conforming drawing primitive definition `text' @ error/draw.c/RenderMVGContent/4337
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in find_bad_exprs(exprs[[i]]) :
  it is not known that wchar_t is Unicode on this platform
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Warning 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 95-96 (manhattanly.Rmd) 
Error: processing vignette 'manhattanly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘manhattanly.Rmd’

SUMMARY: processing the following file failed:
  ‘manhattanly.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning 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]="webshot4257f9213dd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4257f9213dd.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
--- failed re-building ‘manipulateWidgets.Rmd’

SUMMARY: processing the following file failed:
  ‘manipulateWidgets.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   2.5Mb
    doc    1.2Mb
    help   1.6Mb
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    mapdata  33.8Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data          1.0Mb
    doc           1.3Mb
    htmlwidgets   1.6Mb
    libs          3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    mapdata   4.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    java   3.4Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   7.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning 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 (function (filename = "Rplot%03d.png", width = 480, height = 480,  :
  cairo error 'invalid value (typically too big) for the size of the input (surface, pattern, etc.)'
Quitting from lines 39-41 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
unable to start device 'png'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘MBNMAtime.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Reference treatment is `plac`

ET50 parameters (beta.2) are on exponential scale to ensure they take positive values on the natural scale
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   3.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc   6.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   6.0Mb
Package required but not available: ‘gdsfmt’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R     1.4Mb
    doc   3.3Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.1Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.2Mb
Package required but not available: ‘metagenomeSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    help   2.0Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    doc    2.4Mb
Running ‘testthat.R’ [64s/76s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(metR)
  > # library(vdiffr)
  > 
  > test_check("metR")
  ── 1. Error: returns a data.table (@test_ReadNetCDF.R#6)  ──────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
  Backtrace:
   1. testthat::expect_known_output(ReadNetCDF(file), "readnetcdf_default")
   7. metR::ReadNetCDF(file)
   8. ncdf4::nc_open(file)
  
  ── 2. Error: subsetting works (@test_ReadNetCDF.R#11)  ─────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
  Backtrace:
   1. testthat::expect_known_output(...)
   7. metR::ReadNetCDF(file, subset = list(lat = -90:20))
   8. ncdf4::nc_open(file)
  
  Error in R_nc4_open: NetCDF: HDF error
  ── 3. Error: naming works (@test_ReadNetCDF.R#17)  ─────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
  Backtrace:
   1. testthat::expect_true(...)
   4. metR::ReadNetCDF(file, vars = c(air2 = "air"))
   5. ncdf4::nc_open(file)
  
  Error in R_nc4_open: NetCDF: HDF error
  ── 4. Error: different outs work (@test_ReadNetCDF.R#24)  ──────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
  Backtrace:
   1. testthat::expect_s3_class(ReadNetCDF(file), "data.table")
   4. metR::ReadNetCDF(file)
   5. ncdf4::nc_open(file)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 53 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 4 ]
  1. Error: returns a data.table (@test_ReadNetCDF.R#6) 
  2. Error: subsetting works (@test_ReadNetCDF.R#11) 
  3. Error: naming works (@test_ReadNetCDF.R#17) 
  4. Error: different outs work (@test_ReadNetCDF.R#24) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Visualization-tools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Visualization-tools.Rmd’

--- re-building ‘Working-with-data.Rmd’ using rmarkdown
Warning 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 32-40 (Working-with-data.Rmd) 
Error: processing vignette 'Working-with-data.Rmd' failed with diagnostics:
Error in nc_open trying to open file /home/ripley/R/Lib32/metR/extdata/temperature.nc
--- failed re-building ‘Working-with-data.Rmd’

SUMMARY: processing the following file failed:
  ‘Working-with-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    doc    1.1Mb
    libs   1.7Mb
    misc   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
Loading required package: Matrix
Quitting from lines 109-112 (Analysis.Rmd) 
Error: processing vignette 'Analysis.Rmd' failed with diagnostics:
objective in x0 returns NA
--- failed re-building ‘Analysis.Rmd’

--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.

(process:22208): Pango-WARNING **: failed to create cairo scaled font, expect ugly output. the offending font is 'Helvetica Medium 9.9599609375'

(process:22208): Pango-WARNING **: font_face status is: <unknown error status>

(process:22208): Pango-WARNING **: scaled_font status is: invalid matrix (not invertible)

(process:22208): Pango-WARNING **: shaping failure, expect ugly output. shape-engine='BasicEngineFc', font='Helvetica Medium 9.9599609375', text='m'
Loading required package: Matrix
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Level2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
*** This is beta software. Please report any bugs!
*** See the NEWS file for recent changes.
--- finished re-building ‘Level2.Rmd’

SUMMARY: processing the following file failed:
  ‘Analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'REBayes', 'Rmosek'
Packages unavailable to check Rd xrefs: ‘REBayes’, ‘Rmosek’
Error(s) in re-building vignettes:
  ...
--- re-building ‘mixsqp-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Packages suggested but not available for checking:
  'minfi', 'IlluminaHumanMethylation450kmanifest'
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘FSelector’
Packages suggested but not available for checking: 'FSelector', 'RWeka'
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R      1.7Mb
    data   2.4Mb
    help   1.5Mb
Found a ‘configure.in’ file: ‘configure.ac’ has long been preferred.
Error(s) in re-building vignettes:
  ...
--- re-building ‘mnlogit.Rnw’ using Sweave
Package: mnlogit
Version: 1.2.6
Multinomial Logit Choice Models.
Scientific Computing Group, Sentrana Inc.
Loading required package: Formula
Loading required package: zoo

Attaching package: 'zoo'

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

    index

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

    as.Date, as.Date.numeric

Loading required package: lmtest

Attaching package: 'mlogit'

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

    hmftest, scoretest
Running ‘testthat.R’ [15s/197s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > # Run all unit tests
  > 
  > # This is a wrapper around all the tests specified
  > # in the tests/testthat directory. These tests are visible
  > # to users and serve as small examples as well.
  > testthat::test_check("MODISTools")
  Loading required package: MODISTools
  
    |                                                                            
    |                                                                      |   0%
    |                                                                            
    |===================================                                   |  50%
    |                                                                            
    |======================================================================| 100%
  ── 1. Error: test mt_batch_subset() (@test_download_functions.R#232)  ──────────
  one node produced an error: Timeout was reached: [modis.ornl.gov] Resolving timed out after 10000 milliseconds
  Backtrace:
    1. testthat::expect_silent(...)
    9. MODISTools::mt_batch_subset(...)
   10. parallel::parRapply(...)
   12. parallel::clusterApply(...)
   13. parallel:::staticClusterApply(cl, fun, length(x), argfun)
   14. parallel:::checkForRemoteErrors(val)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 25 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: test mt_batch_subset() (@test_download_functions.R#232) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   5.2Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   2.2Mb
Running examples in ‘monoreg-Ex.R’ failed
The error most likely occurred in:

> ### Name: monoreg
> ### Title: Bayesian monotonic regression
> ### Aliases: monoreg
> 
> ### ** Examples
> 
> library(monoreg)
> set.seed(1)
> # nobs <- 1000
> nobs <- 50
> sigma <- 0.01
> x1 <- runif(nobs)
> x2 <- runif(nobs)
> 
> # 6 different monotonic regression surfaces:
> # mu <- sqrt(x1)
> mu <- 0.5 * x1 + 0.5 * x2
> # mu <- pmin(x1, x2)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (x1 + x2 > 1.0)
> # mu <- 0.25 * x1 + 0.25 * x2 + 0.5 * (pmax(x1, x2) > 0.5)
> # mu <- ifelse((x1 - 1.0)^2 + (x2 - 1.0)^2 < 1.0, sqrt(1.0 - (x1 - 1.0)^2 - (x2 - 1.0)^2), 0.0)
> 
> y <- rnorm(nobs, mu, sigma)
> 
> # results <- monoreg(niter=15000, burnin=5000, adapt=5000, refresh=10, 
> results <- monoreg(niter=5000, burnin=2500, adapt=2500, refresh=10, 
+                    thin=5, birthdeath=10, seed=1, rhoa=0.1, rhob=0.1, 
+                    deltai=0.1, drange=2.0, predict=rep(1.0, nobs), 
+                    include=rep(1.0, nobs), response=y, offset=NULL, 
+                    axes=cbind(x1,x2), covariates=rep(1.0, nobs), 
+                    settozero=getcmat(2), package=rep(1,3)) 
Point process configuration:
1 0 1 
1 1 0 
1 0 0 
     
Packages:
1 
0 
Starting Gibbs sampler:

 *** caught segfault ***
address 6, cause 'memory not mapped'

Traceback:
 1: monoreg(niter = 5000, burnin = 2500, adapt = 2500, refresh = 10,     thin = 5, birthdeath = 10, seed = 1, rhoa = 0.1, rhob = 0.1,     deltai = 0.1, drange = 2, predict = rep(1, nobs), include = rep(1,         nobs), response = y, offset = NULL, axes = cbind(x1,         x2), covariates = rep(1, nobs), settozero = getcmat(2),     package = rep(1, 3))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning 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 30-37 (msaR.Rmd) 
Error: processing vignette 'msaR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘msaR.Rmd’

SUMMARY: processing the following file failed:
  ‘msaR.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning 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]="webshot25d23812d97.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot25d23812d97.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

SUMMARY: processing the following file failed:
  ‘msir.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘test-all.R’ [105s/110s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > 
  > library(testthat)
  > 
  > test_check("mudata2")
  Loading required package: mudata2
  
  Attaching package: 'mudata2'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  ── 1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(tf, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 961 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/MultiBD.Rcheck/00install.out’ for details.
Package required but not available: ‘Seurat’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    java  14.0Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    2.5Mb
installed size is 16.4Mb
  sub-directories of 1Mb or more:
    extdata  16.3Mb
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(temp_file_path)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    data   9.5Mb
Running examples in ‘ncdump-Ex.R’ failed
The error most likely occurred in:

> ### Name: NetCDF
> ### Title: Information about a NetCDF file, in convenient form.
> ### Aliases: NetCDF
> 
> ### ** Examples
> 
> rnc <- NetCDF(system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package= "ncdump"))
Error in R_nc4_open: NetCDF: HDF error
Error in ncdf4::nc_open(x) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
Calls: NetCDF -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncdump)
  > 
  > test_check("ncdump")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@testbasic.r#6)  ───────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/ncdump/extdata/S2008001.L3m_DAY_CHL_chlor_a_9km.nc
  Backtrace:
   1. ncdump::NetCDF(ifile)
   2. ncdf4::nc_open(x)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@testbasic.r#6) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘ncmeta-Ex.R’ failed
The error most likely occurred in:

> ### Name: nc_att
> ### Title: NetCDF attributes
> ### Aliases: nc_att nc_att.NetCDF nc_att.character
> 
> ### ** Examples
> 
> f <- system.file("extdata", "S2008001.L3m_DAY_CHL_chlor_a_9km.nc", package = "ncmeta")
> nc_att(f, 0, 0)
Error in RNetCDF::open.nc(x) : NetCDF: HDF error
Calls: nc_att -> nc_att.character -> <Anonymous>
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(ncmeta)
  > skip_on_os("solaris")
  Error: Reason: On Solaris
  Execution halted
Running examples in ‘NCutYX-Ex.R’ failed
The error most likely occurred in:

> ### Name: ancut
> ### Title: Cluster the Columns of Y into K Groups with the Help of External
> ###   Features X.
> ### Aliases: ancut
> 
> ### ** Examples
> 
> #This sets up the initial parameters for the simulation.
> library(MASS)#for mvrnorm
> library(fields)
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.4-0 (2019-11-01) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: ‘spam’

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
> n=30 #Sample size
> B=50 #Number of iterations in the simulated annealing algorithm.
> L=10000 #Temperature coefficient.
> p=50 #Number of columns of Y.
> q=p #Number of columns of X.
> h1=0.15
> h2=0.25
> 
> S=matrix(0.2,q,q)
> S[1:(q/2),(q/2+1):q]=0
> S[(q/2+1):q,1:(q/2)]=0
> S=S-diag(diag(S))+diag(q)
> 
> mu=rep(0,q)
> 
> W0=matrix(1,p,p)
> W0[1:(p/2),1:(p/2)]=0
> W0[(p/2+1):p,(p/2+1):p]=0
> Denum=sum(W0)
> 
> B2=matrix(0,q,p)
> for (i in 1:(p/2)){
+    B2[1:(q/2),i]=runif(q/2,h1,h2)
+    in1=sample.int(q/2,6)
+    B2[-in1,i]=0
+ }
> 
> for (i in (p/2+1):p){
+    B2[(q/2+1):q,i]=runif(q/2,h1,h2)
+    in2=sample(seq(q/2+1,q),6)
+    B2[-in2,i]=0
+ }
> 
> X=mvrnorm(n, mu, S)
> Z=X%*%B2
> Y=Z+matrix(rnorm(n*p,0,1),n,p)
> #Our method
> Res=ancut(Y=Y,X=X,B=B,L=L,alpha=0,ncv=3)
Error in if (J2 > J) { : missing value where TRUE/FALSE needed
Calls: ancut
Execution halted
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/NestedCategBayesImpute.Rcheck/00install.out’ for details.
Running examples in ‘NetMix-Ex.R’ failed
The error most likely occurred in:

> ### Name: covFX
> ### Title: Generate estimated monadic covariate effects for estimated mmsbm
> ###   model
> ### Aliases: covFX
> 
> ### ** Examples
> 
> library(NetMix)
> ## Load datasets
> data("lazega_dyadic")
> data("lazega_monadic")
> ## Estimate model with 2 groups
> set.seed(123)
> lazega_mmsbm <- mmsbm(SocializeWith ~ Coworkers,
+                       ~  School + Practice + Age,
+                       senderID = "Lawyer1",
+                       receiverID = "Lawyer2",
+                       nodeID = "Lawyer",
+                       data.dyad = lazega_dyadic,
+                       data.monad = lazega_monadic,
+                       n.blocks = 2)
Error in .mmsbm_fit(t(Z), t(X), Y, t_id_d, t_id_n, nodes_pp, nt_id, mu_b,  : 
  Phi value became NaN
Calls: mmsbm -> .mmsbm_fit
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘NetRep.Rmd’ using rmarkdown
Warning 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 286-289 (NetRep.Rmd) 
Error: processing vignette 'NetRep.Rmd' failed with diagnostics:
dim(X) must have a positive length
--- failed re-building ‘NetRep.Rmd’

SUMMARY: processing the following file failed:
  ‘NetRep.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    data   7.8Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introducing_nhanesA.Rmd’ using rmarkdown
Warning 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 92-98 (Introducing_nhanesA.Rmd) 
Error: processing vignette 'Introducing_nhanesA.Rmd' failed with diagnostics:
Timeout was reached: [wwwn.cdc.gov] Resolving timed out after 10000 milliseconds
--- failed re-building ‘Introducing_nhanesA.Rmd’

SUMMARY: processing the following file failed:
  ‘Introducing_nhanesA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.9Mb
installed size is 27.5Mb
  sub-directories of 1Mb or more:
    CppCode  10.4Mb
    R         6.1Mb
    include   5.3Mb
    libs      2.8Mb
    tests     1.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘geocode.Rmd’

SUMMARY: processing the following file failed:
  ‘geocode.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘NLMR-Ex.R’ failed
The error most likely occurred in:

> ### Name: nlm_randomcluster
> ### Title: nlm_randomcluster
> ### Aliases: nlm_randomcluster
> 
> ### ** Examples
> 
> # simulate random clustering
> random_cluster <- nlm_randomcluster(ncol = 30, nrow = 30,
+                                      p = 0.4,
+                                      ai = c(0.25, 0.25, 0.5))
Loading required namespace: igraph
Failed with error:  ‘there is no package called ‘igraph’’
Error in .local(x, ...) : 
  you need to install the igraph package to be able to use this function
Calls: nlm_randomcluster -> <Anonymous> -> <Anonymous> -> .local
Execution halted
Running ‘testthat.R’ [42s/48s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  ── 1. Error: (unknown) (@test_randomcluster.R#4)  ──────────────────────────────
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘nlrx-Ex.R’ failed
The error most likely occurred in:

> ### Name: nldoc
> ### Title: Create NetLogo documentation
> ### Aliases: nldoc
> 
> ### ** Examples
> 
> 
> # List model files (.nls subfiles are also supported)
> modelfiles <- c("https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nlogo",
+                 "https://raw.githubusercontent.com/nldoc/nldoc_pg/master/WSP.nls")
> 
> # Define output directory:
> outdir <- tempdir()  # adjust path to your needs
> 
> # Create documentation:
> nldoc(modelfiles = modelfiles,
+       infotab=TRUE,
+       gui=TRUE,
+       bs=TRUE,
+       outpath = outdir,
+       output_format = "html",
+       number_sections = TRUE,
+       theme = "cosmo",
+       date = date(),
+       toc = TRUE)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data      4.4Mb
    doc       1.2Mb
    reports   3.8Mb
Found the following significant warnings:
  WrapperNMFGPU.cpp:96:12: warning: converting ‘false’ to pointer type for argument 1 of ‘std::__cxx11::basic_string<_CharT, _Traits, _Alloc>::basic_string(const _CharT*, const _Alloc&) [with _CharT = char; _Traits = std::char_traits<char>; _Alloc = std::allocator<char>]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/nmfgpu4R.Rcheck/00install.out’ for details.
Running examples in ‘NMF-Ex.R’ failed
The error most likely occurred in:

> ### Name: NMFfitX-class
> ### Title: Virtual Class to Handle Results from Multiple Runs of NMF
> ###   Algorithms
> ### Aliases: NMFfitX-class
> 
> ### ** Examples
> 
> ## Don't show: 
> # roxygen generated flag
> options(R_CHECK_RUNNING_EXAMPLES_=TRUE)
> ## End(Don't show)
> 
> # generate a synthetic dataset with known classes
> n <- 20; counts <- c(5, 2, 3);
> V <- syntheticNMF(n, counts)
> 
> # perform multiple runs of one algorithm (default is to keep only best fit)
> res <- nmf(V, 3, nrun=3)
# NOTE - CRAN check detected: limiting maximum number of cores [2/16]
Error in big.matrix(nrow = nrow(x), ncol = ncol(x), type = type, init = NULL,  : 
  Error: memory could not be allocated for instance of type big.matrix
Calls: nmf ... gVariable -> <Anonymous> -> <Anonymous> -> big.matrix
Timing stopped at: 0.032 0.043 0.172
Execution halted
Package unavailable to check Rd xrefs: ‘redux’
Running examples in ‘norm2-Ex.R’ failed
The error most likely occurred in:

> ### Name: emNorm
> ### Title: EM algorithm for incomplete multivariate normal data
> ### Aliases: emNorm emNorm.default emNorm.formula emNorm.norm
> ### Keywords: multivariate NA
> 
> ### ** Examples
> 
> ## run EM for marijuana data with strict convergence criterion
> data(marijuana)
> result <- emNorm(marijuana, criterion=1e-06)

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

Traceback:
 1: emNorm.default(marijuana, criterion = 1e-06)
 2: emNorm(marijuana, criterion = 1e-06)
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  9.6Mb
  sub-directories of 1Mb or more:
    doc   8.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NormalizeMets_vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 192-194 (NormalizeMets_vignette.Rmd) 
Error: processing vignette 'NormalizeMets_vignette.Rmd' failed with diagnostics:
Saving a widget with selfcontained = TRUE requires pandoc. For details see:
https://github.com/rstudio/rmarkdown/blob/master/PANDOC.md
--- failed re-building ‘NormalizeMets_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘NormalizeMets_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘noteMD-Ex.R’ failed
The error most likely occurred in:

> ### Name: note_in_html
> ### Title: Print text input in html
> ### Aliases: note_in_html
> 
> ### ** Examples
> 
> note_in_html("Please write note using **Markdown** syntax! ")
sh: +RTS:  not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    7.5Mb
    libs   1.0Mb
installed size is 39.1Mb
  sub-directories of 1Mb or more:
    extdata  39.0Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R            1.7Mb
    test_files   4.4Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    data   1.0Mb
    doc    2.8Mb
    help   2.6Mb
Packages suggested but not available for checking: 'RMark', 'R2ucare'
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R        2.7Mb
    data     1.0Mb
    libs     3.7Mb
    models   4.5Mb
Running examples in ‘OpenMx-Ex.R’ failed
The error most likely occurred in:

> ### Name: mxModelAverage
> ### Title: Information-Theoretic Model-Averaging and Multimodel Inference
> ### Aliases: mxModelAverage omxAkaikeWeights omxAICWeights
> 
> ### ** Examples
> 
> require(OpenMx)
> data(demoOneFactor)
> factorModel1 <- mxModel(
+ 	"OneFactor1",
+ 	mxMatrix(
+ 		"Full", 5, 1, values=0.8, 
+ 		labels=paste("a",1:5,sep=""),
+ 		free=TRUE, name="A"),
+ 	mxMatrix(
+ 		"Full", 5, 1, values=1,
+ 		labels=paste("u",1:5,sep=""),
+ 		free=TRUE, name="Udiag"),
+ 	mxMatrix(
+ 		"Symm", 1, 1, values=1,
+ 		free=FALSE, name="L"),
+ 	mxAlgebra(vec2diag(Udiag),name="U"),
+ 	mxAlgebra(A %*% L %*% t(A) + U, name="R"),
+ 	mxExpectationNormal(
+ 		covariance = "R",
+ 		dimnames = names(demoOneFactor)),
+ 	mxFitFunctionML(),
+ 	mxData(cov(demoOneFactor), type="cov", numObs=500))
> factorFit1 <- mxRun(factorModel1)
Running OneFactor1 with 10 parameters
Error: C stack usage  203986068 is too close to the limit
Error: The job for model 'OneFactor1' exited abnormally with the error message: User interrupt
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    java     1.3Mb
    models   6.1Mb
Packages suggested but not available for checking:
  'gurobi', 'Rsymphony', 'lpsymphony'
File ‘OriGen/libs/OriGen.so’:
  Found ‘__f90_close’, possibly from ‘close’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_esfr’, possibly from ‘read’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_open’, possibly from ‘open’ (Fortran)
    Object: ‘OriGen.o’
  Found ‘__f90_rewind’, possibly from ‘rewind’ (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  7.3Mb
  sub-directories of 1Mb or more:
    R       1.1Mb
    nifti   4.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc   7.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘outliertree-Ex.R’ failed
The error most likely occurred in:

> ### Name: outlier.tree
> ### Title: Outlier Tree
> ### Aliases: outlier.tree
> 
> ### ** Examples
> 
> library(outliertree)
> 
> ### example dataset with interesting outliers
> data(hypothyroid)
> 
> ### fit the model and get a print of outliers
> model <- outlier.tree(hypothyroid, outliers_print=10, save_outliers=TRUE)

 *** caught segfault ***
address fffffff7, cause 'memory not mapped'
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(oxcAAR)
  > 
  > test_check("oxcAAR")
  sh: /home/ripley/R/packages/tests32/oxcAAR.Rcheck/tests/testthat/ox_output.js: cannot execute
  ── 1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `quickSetupOxcal()` threw an error.
  Message: argument is of length zero
  Class:   simpleError/error/condition
  Backtrace:
   1. testthat::expect_error(quickSetupOxcal(), NA)
   6. oxcAAR::quickSetupOxcal()
  
  ── 2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  dir.exists("OxCal/bin/") isn't true.
  
  ── 3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_util
  `%in%`(...) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 94 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#30) 
  2. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#31) 
  3. Failure: quickSetupOxcal downloads oxcal and sets correct path (@test_utility_functions.R#32) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic-usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 24-30 (basic-usage.Rmd) 
Error: processing vignette 'basic-usage.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘basic-usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic-usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data        1.6Mb
    localdata   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘pandocfilters.Rnw’ using knitr
Quitting from lines 68-69 (pandocfilters.Rnw) 
Error: processing vignette 'pandocfilters.Rnw' failed with diagnostics:
error in running command: 'Illegal seek'
--- failed re-building ‘pandocfilters.Rnw’

SUMMARY: processing the following file failed:
  ‘pandocfilters.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction-to-parcoords-.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-parcoords-.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/pathfindR.Rcheck/00install.out’ for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.2Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc        1.3Mb
    examples   1.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       2.0Mb
    extdata   3.1Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    1.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   8.4Mb
Package unavailable to check Rd xrefs: ‘tesseract’
Running examples in ‘pense-Ex.R’ failed
The error most likely occurred in:

> ### Name: coef.pense
> ### Title: Extract Model Coefficients
> ### Aliases: coef.pense
> 
> ### ** Examples
> 
> # Generate data with highly correlated groups of variables and some outliers
> set.seed(12345)
> n <- 50
> n_out <- 3
> p <- 20
> x <- 1 + matrix(rnorm(n * p), ncol = p)
> x[, 2] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 3] <- x[, 1] + rnorm(n, sd = 0.01)
> x[, 5] <- x[, 4] + rnorm(n, sd = 0.01)
> x[, 6] <- x[, 4] + rnorm(n, sd = 0.01)
> 
> y <- x %*% c(rep(c(2, 5), each = 3), numeric(p - 6)) + rnorm(n)
> 
> y[seq_len(n_out)] <- rnorm(n_out, -100, sd = 3)
> 
> # Compute the PENSE estimator
> set.seed(1234)
> est_en <- pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)

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

Traceback:
 1: enpy_exact(x, y, alpha, lambda, options, en_options)
 2: enpy(std_data$xs, std_data$yc, alpha, lambda, delta = pense_options$bdp,     cc = pense_options$cc, options = initest_options, en_options = en_options)
 3: pense_init_cold(x = x_train, y = y_train, lambda = job$lambda,     ...)
 4: FUN(X[[i]], ...)
 5: cluster$lapply(jobs_cold_est, get_cold_est, alpha = alpha, standardize = standardize,     pense_options = options, initest_options = init_options,     en_options = en_options)
 6: doTryCatch(return(expr), name, parentenv, handler)
 7: tryCatchOne(expr, names, parentenv, handlers[[1L]])
 8: tryCatchList(expr, classes, parentenv, handlers)
 9: tryCatch({    cold_inits <- cluster$lapply(jobs_cold_est, get_cold_est,         alpha = alpha, standardize = standardize, pense_options = options,         initest_options = init_options, en_options = en_options)}, error = function(e) {    cluster$stopCluster()    stop(e)})
10: pense(x, y, alpha = 0.5, warm_reset = 1, cv_k = 3)
An irrecoverable exception occurred. R is aborting now ...
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R      4.5Mb
    data   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-59 (Introduction.Rmd) 
Error: processing vignette 'Introduction.Rmd' failed with diagnostics:
EXPR must be a length 1 vector
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   5.5Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc       1.6Mb
    extdata   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-27 (Advanced_Usage.Rmd) 
Error: processing vignette 'Advanced_Usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning 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 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   2.0Mb
    doc    3.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
grid object contains more than 50000 pixels
increase `maxpixels` for a finer resolution
Quitting from lines 496-508 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Timeout was reached: [upwell.pfeg.noaa.gov] Operation timed out after 10000 milliseconds with 0 out of 0 bytes received
--- failed re-building ‘using_plotdap.Rmd’

SUMMARY: processing the following file failed:
  ‘using_plotdap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    R             1.1Mb
    htmlwidgets   3.4Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   6.4Mb
Running ‘testthat.R’ [53s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmml, quietly = T)
  > 
  > test_check("pmml")
  Error: segfault from C stack overflow
  Execution halted
Running ‘testthat.R’ [50s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(pmultinom)
  > 
  > test_check("pmultinom")
  ── 1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertp
  invert.pmultinom(...) not equal to 0.
  1/1 mismatches
  [1] 3 - 0 == 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1561 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Correct behavior when target probability is 0 or 1 (@test_invertpmultinom.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   6.1Mb
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in check_codoc(x, as.pairlist(as.alist.call(y[-1L]))) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Warning in .arg_names_from_call(e[-1L]) :
  it is not known that wchar_t is Unicode on this platform
Functions with \usage entries need to have the appropriate \alias
entries, and all their arguments documented.
The \usage entries must correspond to syntactically valid R code.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R      7.0Mb
    data   2.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   5.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘burkina-faso-females.Rnw’ using Sweave
Loading required package: coda
Loading required package: gdata
gdata: read.xls support for 'XLS' (Excel 97-2004) files
gdata: ENABLED.

gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.

gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.

Attaching package: ‘gdata’

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

    nobs

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

    object.size

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

    startsWith

Calculating life expectancy at birth ...
... done
Calculating net number of migrants ...
... done
Error: processing vignette 'burkina-faso-females.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'burkina-faso-females.tex' failed.
BibTeX errors:
The top-level auxiliary file: burkina-faso-females.aux
I couldn't open style file apa.bst
---line 19 of file burkina-faso-females.aux
 : \bibstyle{apa
 :              }
I'm skipping whatever remains of this command
I found no style file---while reading file burkina-faso-females.aux
--- failed re-building ‘burkina-faso-females.Rnw’

SUMMARY: processing the following file failed:
  ‘burkina-faso-females.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ROI.plugin.symphony’
Package suggested but not available for checking: ‘CVXR’
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    java   5.7Mb
Running ‘test-all.R’ [87s/95s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > test_check("POUMM")
  Loading required package: POUMM
  Loading required package: Rcpp
    generate 10000 samples 
    generate 10000 samples 
    generate 10000 samples 
  ── 1. Failure: fastLik(C++) vs algebraic lik (@test-lik.R#63)  ─────────────────
  likPOUMMGivenTreeVTipsC(...) not equivalent to dVTipsGivenTreePOUMMg0Alg(...).
  1/1 mismatches
  [1] -2546754 - -2898 == -2543856
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 30 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: fastLik(C++) vs algebraic lik (@test-lik.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Powerful_MaxEigenpair.Rmd’ using knitr
Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-3'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-5'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-6'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-7'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-8'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-9'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-11'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-13'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'unnamed-chunk-14'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 208-221 (Powerful_MaxEigenpair.Rmd) 
Error: processing vignette 'Powerful_MaxEigenpair.Rmd' failed with diagnostics:
cannot allocate vector of size 1.7 Gb
--- failed re-building ‘Powerful_MaxEigenpair.Rmd’

SUMMARY: processing the following file failed:
  ‘Powerful_MaxEigenpair.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc  11.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning 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: 'heatmap' objects don't have these attributes: 'showlegend'
Valid attributes include:
'type', 'visible', 'opacity', 'name', 'uid', 'ids', 'customdata', 'meta', 'hoverinfo', 'hoverlabel', 'stream', 'transforms', 'uirevision', 'z', 'x', 'x0', 'dx', 'y', 'y0', 'dy', 'text', 'hovertext', 'transpose', 'xtype', 'ytype', 'zsmooth', 'connectgaps', 'xgap', 'ygap', 'zhoverformat', 'hovertemplate', 'zauto', 'zmin', 'zmax', 'zmid', 'colorscale', 'autocolorscale', 'reversescale', 'showscale', 'colorbar', 'coloraxis', 'xcalendar', 'ycalendar', 'xaxis', 'yaxis', 'idssrc', 'customdatasrc', 'metasrc', 'hoverinfosrc', 'zsrc', 'xsrc', 'ysrc', 'textsrc', 'hovertextsrc', 'hovertemplatesrc', 'key', 'set', 'frame', 'transforms', '_isNestedKey', '_isSimpleKey', '_isGraticule', '_bbox'

Warning in normalizePath(f2) :
  path[1]="webshot3ce915817a3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3ce915817a3.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PPQplan-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of ‘Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]’ [-Wconversion-null]
See ‘/home/ripley/R/packages/tests32/PPRL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘Rmosek’
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: predict3d
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'gurobi', 'lpsymphony', 'Rsymphony'
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning 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 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   4.4Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    doc           9.3Mb
    htmlwidgets   2.7Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Running examples in ‘profile-Ex.R’ failed
The error most likely occurred in:

> ### Name: read_rprof
> ### Title: File I/O for profiler data
> ### Aliases: read_rprof read_pprof write_rprof write_pprof
> 
> ### ** Examples
> 
> rprof_file <- system.file("samples/rprof/1.out", package = "profile")
> ds <- read_rprof(rprof_file)
> ds
Profile data: 22 samples
> pprof_file <- tempfile("profile", fileext = ".pb.gz")
> write_pprof(ds, pprof_file)
Error: Package RProtoBuf is required to read pprof files.
Backtrace:
    █
 1. └─profile::write_pprof(ds, pprof_file)
 2.   └─profile:::ds_to_msg(x)
 3.     └─profile:::provide_proto()
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    extdata   8.2Mb
Loading this package had a fatal error status code 1
Loading log:
Loading required package: Rcpp
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: ggplot2
Loading required package: scales
Error: package or namespace load failed for ‘promotionImpact’:
 .onLoad failed in loadNamespace() for 'prophet', details:
  call: sink(type = "output")
  error: invalid connection
In addition: Warning message:
In system(cmd, intern = !verbose) :
  running command '/home/ripley/R/cc/bin/R CMD SHLIB filec94427c777.cpp 2> filec94427c777.cpp.err.txt' had status 1 and error message 'Illegal seek'
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data      1.8Mb
    extdata   2.8Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    data   1.0Mb
    doc    2.7Mb
    help   1.0Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    dict   5.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc        4.8Mb
    examples   2.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘PWFSLSmoke.Rmd’

SUMMARY: processing the following file failed:
  ‘PWFSLSmoke.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   7.3Mb
Running examples in ‘pyinit-Ex.R’ failed
The error most likely occurred in:

> ### Name: pyinit
> ### Title: PY (Pena-Yohai) initial estimates for S-estimates of regression
> ### Aliases: pyinit
> 
> ### ** Examples
> 
> # generate a simple synthetic data set for a linear regression model
> # with true regression coefficients all equal to one "(1, 1, 1, 1, 1)"
> set.seed(123)
> x <- matrix(rnorm(100*4), 100, 4)
> y <- rnorm(100) + rowSums(x) + 1
> # add masked outliers
> a <- svd(var(x))$v[,4]
> x <- rbind(x, t(outer(a, rnorm(20, mean=4, sd=1))))
> y <- c(y, rnorm(20, mean=-2, sd=.2))
> 
> # these outliers are difficult to find
> plot(lm(y~x), ask=FALSE)
> 
> # use pyinit to obtain estimated regression coefficients
> tmp <- pyinit(x=x, y=y, resid_keep_method='proportion', psc_keep = .5, resid_keep_prop=.5)

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

Traceback:
 1: pyinit(x = x, y = y, resid_keep_method = "proportion", psc_keep = 0.5,     resid_keep_prop = 0.5)
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    gui          1.3Mb
    staticdocs   3.4Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    data  12.9Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    R         1.9Mb
    contrib   3.7Mb
    doc       3.3Mb
    libs      1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Qtools.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-146 (Qtools.Rmd) 
Error: processing vignette 'Qtools.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘Qtools.Rmd’

SUMMARY: processing the following file failed:
  ‘Qtools.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    help   1.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘quadmesh.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-35 (quadmesh.Rmd) 
Error: processing vignette 'quadmesh.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quadmesh.Rmd’

--- re-building ‘topography.Rmd’ using rmarkdown
Warning 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 19-33 (topography.Rmd) 
Error: processing vignette 'topography.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘topography.Rmd’

SUMMARY: processing the following files failed:
  ‘quadmesh.Rmd’ ‘topography.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 83-117 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   1.4Mb
    libs   1.2Mb
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
Warning in deparse(e[[2L]]) :
  it is not known that wchar_t is Unicode on this platform
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Running examples in ‘r2pmml-Ex.R’ failed
The error most likely occurred in:

> ### Name: decorate.glmnet
> ### Title: Decorates a "glmnet" object with a "lambda.s" element.
> ### Aliases: decorate.glmnet
> 
> ### ** Examples
> 
> library("glmnet")
Loading required package: Matrix
Loaded glmnet 3.0-1

> library("r2pmml")
> 
> data(iris)
> iris_x = as.matrix(iris[, -ncol(iris)])
> iris_y = iris[, ncol(iris)]
> iris.glmnet = glmnet(x = iris_x, y = iris_y, family = "multinomial")
> iris.glmnet = decorate(iris.glmnet, lambda.s = iris.glmnet$lambda[49])
> r2pmml(iris.glmnet, file.path(tempdir(), "Iris-GLMNet.pmml"))
Exception in thread "main" java.lang.UnsupportedClassVersionError: org/jpmml/rexp/Main : Unsupported major.minor version 52.0
	at java.lang.ClassLoader.defineClass1(Native Method)
	at java.lang.ClassLoader.defineClass(ClassLoader.java:800)
	at java.security.SecureClassLoader.defineClass(SecureClassLoader.java:142)
	at java.net.URLClassLoader.defineClass(URLClassLoader.java:449)
	at java.net.URLClassLoader.access$100(URLClassLoader.java:71)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:361)
	at java.net.URLClassLoader$1.run(URLClassLoader.java:355)
	at java.security.AccessController.doPrivileged(Native Method)
	at java.net.URLClassLoader.findClass(URLClassLoader.java:354)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:425)
	at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:308)
	at java.lang.ClassLoader.loadClass(ClassLoader.java:358)
	at sun.launcher.LauncherHelper.checkAndLoadMain(LauncherHelper.java:482)
Error in .convert(tempfile, file, converter, converter_classpath, verbose) : 
  The JPMML-R conversion application has failed (error code 1). The Java executable should have printed more information about the failure into its standard output and/or standard error streams
Calls: r2pmml -> tryCatch -> tryCatchList -> main -> .convert
Execution halted
Package unavailable to check Rd xrefs: ‘BRugs’
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
Warning 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
Quitting from lines 285-287 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘RAbHIT-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RAbHIT-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    6.0Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    app   6.1Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      2.3Mb
    extdata   1.5Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    api           3.0Mb
    htmlwidgets   7.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘randomNames.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-26 (randomNames.Rmd) 
Error: processing vignette 'randomNames.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘randomNames.Rmd’

SUMMARY: processing the following file failed:
  ‘randomNames.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [179s/183s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(randomsearch)
  Loading required package: ParamHelpers
  Loading required package: smoof
  Loading required package: BBmisc
  
  Attaching package: 'BBmisc'
  
  The following object is masked from 'package:base':
  
      isFALSE
  
  Loading required package: checkmate
  > 
  > test_check("randomsearch")
  Error : [ENOENT] Failed to stat '/tmp/RtmpRLaGQn/working_dir/RtmpU1aOmy/file30655f497c95/1_9': no such file or directory
  ── 1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#
  [ENOENT] Failed to stat '/tmp/RtmpRLaGQn/working_dir/RtmpU1aOmy/file30655f497c95/1_9': no such file or directory
  
  Backtrace:
   1. randomsearch::randomsearch(...)
   2. randomsearch:::randomsearch.smoof_function(...)
   3. parallelMap::parallelMap(...)
   4. parallelMap:::checkResultsAndStopWithErrorsMessages(res)
   5. parallelMap:::stopWithJobErrorMessages(...)
   6. BBmisc::stopf(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 69 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: parallel randomsearch works with parallelMap (@test_randomsearch.R#83) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘rapidraker-Ex.R’ failed
The error most likely occurred in:

> ### Name: rapidrake
> ### Title: Rapid RAKE
> ### Aliases: rapidrake
> 
> ### ** Examples
> 
> rapidrake(txt = "some text that has great keywords")
Error in .jfindClass(as.character(class)) : 
  java.lang.UnsupportedClassVersionError: opennlp/tools/stemmer/snowball/SnowballStemmer : Unsupported major.minor version 52.0
Calls: rapidrake ... <Anonymous> -> <Anonymous> -> jclassName -> .jfindClass
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rapidraker)
  > 
  > test_check("rapidraker")
  ── 1. Error: (unknown) (@test-rapidrake.R#3)  ──────────────────────────────────
  no field, method or inner class called 'handled' 
  Backtrace:
    1. testthat::test_check("rapidraker")
    2. testthat:::test_package_dir(...)
    3. testthat::test_dir(...)
    4. testthat:::test_files(...)
   10. base::lapply(...)
   11. testthat:::FUN(X[[i]], ...)
   17. testthat::source_file(...)
   18. testthat:::test_code(NULL, exprs, env)
   27. [ base::eval(...) ] with 1 more call
   29. testthat::test_that(...)
   30. testthat:::test_code(desc, code, env = parent.frame())
   31. base::tryCatch(...)
   32. base:::tryCatchList(expr, classes, parentenv, handlers)
   35. base:::tryCatchList(expr, names[-nh], parentenv, handlers[-nh])
   36. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   37. value[[3L]](cond)
   40. rJava:::`$.Throwable`(e, "handled")
   41. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-rapidrake.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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: 'lubridate'

The following objects are masked from 'package:data.table':

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

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

    date

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'playwith', 'rggobi', 'RGtk2Extras'
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   3.1Mb
    etc    2.2Mb
    po     1.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘raustats_introduction.Rmd’ using rmarkdown
Warning 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: readxl
Attaching package: 'raustats'
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Jun%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Jun%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/6401.0Sep%202019?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Dec%202017?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Sep%202017?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/1270.0.55.001July%202016?OpenDocument
Navigating to /AUSSTATS/abs@.nsf/DetailsPage/5206.0Jun%202019?OpenDocument
Quitting from lines 636-639 (raustats_introduction.Rmd) 
Error: processing vignette 'raustats_introduction.Rmd' failed with diagnostics:
Timeout was reached: [stat.data.abs.gov.au] Resolving timed out after 10010 milliseconds
--- failed re-building ‘raustats_introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘raustats_introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘av’
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   1.7Mb
Running examples in ‘rbi.helpers-Ex.R’ failed
The error most likely occurred in:

> ### Name: DIC
> ### Title: Compute Deviance Information Criterion (DIC) for a libbi model
> ### Aliases: DIC DIC.libbi
> 
> ### ** Examples
> 
> example_run <- bi_read(system.file(package="rbi", "example_output.nc"))
Error in R_nc4_open: NetCDF: HDF error
Error in nc_open(tools::file_path_as_absolute(x)) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
Calls: bi_read -> bi_open -> nc_open
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rbi.helpers)
  Loading required package: rbi
  
  Attaching package: 'rbi'
  
  The following objects are masked from 'package:stats':
  
      filter, optimise, predict, simulate, update
  
  The following object is masked from 'package:utils':
  
      fix
  
  The following object is masked from 'package:base':
  
      sample
  
  > 
  > test_check("rbi.helpers")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@test-DIC.r#3)  ────────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
  Backtrace:
   1. rbi::bi_read(system.file(package = "rbi", "example_output.nc"))
   2. rbi:::bi_open(x)
   3. ncdf4::nc_open(tools::file_path_as_absolute(x))
  
  Error in R_nc4_open: NetCDF: HDF error
  ── 2. Error: (unknown) (@test-adapt.r#4)  ──────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
  Backtrace:
   1. rbi::bi_read(system.file(package = "rbi", "example_output.nc"))
   2. rbi:::bi_open(x)
   3. ncdf4::nc_open(tools::file_path_as_absolute(x))
  
  Error in R_nc4_open: NetCDF: HDF error
  ── 3. Error: (unknown) (@test-times.r#3)  ──────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
  Backtrace:
   1. rbi::bi_read(system.file(package = "rbi", "example_output.nc"))
   2. rbi:::bi_open(x)
   3. ncdf4::nc_open(tools::file_path_as_absolute(x))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: (unknown) (@test-DIC.r#3) 
  2. Error: (unknown) (@test-adapt.r#4) 
  3. Error: (unknown) (@test-times.r#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in ‘rbi-Ex.R’ failed
The error most likely occurred in:

> ### Name: attach_data
> ### Title: Attach a new file or data set to a 'libbi' object
> ### Aliases: attach_data attach_data.libbi
> 
> ### ** Examples
> 
> bi <- libbi(model = system.file(package="rbi", "PZ.bi"))
> example_output <- bi_read(system.file(package="rbi", "example_output.nc"))
Error in R_nc4_open: NetCDF: HDF error
Error in nc_open(tools::file_path_as_absolute(x)) : 
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
Calls: bi_read -> bi_open -> nc_open
Execution halted
Running ‘testthat.R’ [17s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rbi)
  
  Attaching package: 'rbi'
  
  The following objects are masked from 'package:stats':
  
      filter, optimise, predict, simulate, update
  
  The following object is masked from 'package:utils':
  
      fix
  
  The following object is masked from 'package:base':
  
      sample
  
  > 
  > test_check("rbi")
  Error in R_nc4_open: NetCDF: HDF error
  ── 1. Error: (unknown) (@test-samples.r#4)  ────────────────────────────────────
  Error in nc_open trying to open file /home/ripley/R/Lib32/rbi/example_output.nc
  Backtrace:
   1. rbi::bi_read(system.file(package = "rbi", "example_output.nc"))
   2. rbi:::bi_open(x)
   3. ncdf4::nc_open(tools::file_path_as_absolute(x))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 145 | SKIPPED: 6 | WARNINGS: 32 | FAILED: 1 ]
  1. Error: (unknown) (@test-samples.r#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 23.4Mb
  sub-directories of 1Mb or more:
    cont  23.4Mb
Running examples in ‘rchallenge-Ex.R’ failed
The error most likely occurred in:

> ### Name: icon
> ### Title: HTML code for icons. Currently only supports Font Awesome icons.
> ### Aliases: icon
> 
> ### ** Examples
> 
> rmd <- '
+ ```{r}
+ library(rchallenge)
+ ```
+ <link rel="stylesheet" 
+  href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
+ `r icon("fa-user")`
+ `r icon("fa-user fa-lg")`
+ `r icon("fa-user fa-2x")`
+ `r icon("fa-user fa-3x")`
+ `r icon("fa-user fa-3x fa-border")`
+ '
> file <- tempfile()
> cat(rmd, file=file)
> writeLines(readLines(file))

```{r}
library(rchallenge)
```
<link rel="stylesheet" 
 href="https://maxcdn.bootstrapcdn.com/font-awesome/4.6.3/css/font-awesome.min.css">
`r icon("fa-user")`
`r icon("fa-user fa-lg")`
`r icon("fa-user fa-2x")`
`r icon("fa-user fa-3x")`
`r icon("fa-user fa-3x fa-border")`
> rmarkdown::render(file)
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Running examples in ‘RclusTool-Ex.R’ failed
The error most likely occurred in:

> ### Name: RclusToolGUI
> ### Title: Username and user type selection
> ### Aliases: RclusToolGUI
> 
> ### ** Examples
> 
> RclusToolGUI()
Error in if (RclusTool.env$gui$operating.system == "windows") { : 
  argument is of length zero
Calls: RclusToolGUI
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   5.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   3.3Mb
    po    2.2Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    corpora   8.2Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/RcppAnnoy.Rcheck/00install.out’ for details.
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘RcppCNPy-intro.Rmd’ using rmarkdown
Warning 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 95-104 (RcppCNPy-intro.Rmd) 
Error: processing vignette 'RcppCNPy-intro.Rmd' failed with diagnostics:
Python shared library not found, Python bindings not loaded.
--- failed re-building ‘RcppCNPy-intro.Rmd’

--- re-building ‘UsingReticulate.Rmd’ using rmarkdown
Warning 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 84-94 (UsingReticulate.Rmd) 
Error: processing vignette 'UsingReticulate.Rmd' failed with diagnostics:
Python shared library not found, Python bindings not loaded.
--- failed re-building ‘UsingReticulate.Rmd’

SUMMARY: processing the following files failed:
  ‘RcppCNPy-intro.Rmd’ ‘UsingReticulate.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    include   7.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    include   1.5Mb
    lib       3.0Mb
    libs      1.2Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    include   5.8Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc       1.2Mb
    include   6.6Mb
Running ‘testthat.R’ [18s/21s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(RCSF)
  > 
  > test_check("RCSF")
  ── 1. Failure: csf algorithm works (@test-CSF.R#8)  ────────────────────────────
  length(id_ground) not equal to `expected`.
  1/1 mismatches
  [1] 15456 - 15453 == 3
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: csf algorithm works (@test-CSF.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No methods found in package 'redland' for request: 'getNextResult' when loading 'rdflib'

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rdf_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rdf_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    java  10.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’ using rmarkdown
Warning 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: rJava
Loading required package: Rdroolsjars

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: 'purrr'

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 in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
Warning: filter_() is deprecated. 
Please use filter() instead

The 'programming' vignette or the tidyeval book can help you
to program with filter() : https://tidyeval.tidyverse.org
This warning is displayed once per session.
Warning in if (class(intermediateOutput) == "list") { :
  the condition has length > 1 and only the first element will be used
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:
there is no package called 'webshot'
--- failed re-building ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

SUMMARY: processing the following file failed:
  ‘Executing_Business_Rules_At_Scale_With_RDrools_using_Drools.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   8.9Mb
Package suggested but not available for checking: ‘Rsymphony’

Package which this enhances but not available for checking: ‘Rcplex’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    doc   8.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning 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: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
Warning 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: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘respirometry-Ex.R’ failed
The error most likely occurred in:

> ### Name: calc_MO2
> ### Title: Calculate metabolic rate
> ### Aliases: calc_MO2
> 
> ### ** Examples
> 
> # get O2 data
> file <- system.file('extdata', 'witrox_file.txt', package = 'respirometry')
> o2_data <- na.omit(import_witrox(file, split_channels = TRUE)$CH_4)
Warning in strsplit(raw, split = "\r\n", fixed = T) :
  input string 1 is invalid UTF-8
Error in grep("Date &Time [", f[1:20], fixed = TRUE):length(f) : 
  argument of length 0
Calls: na.omit -> import_witrox
Execution halted
Running examples in ‘revgeo-Ex.R’ failed
The error most likely occurred in:

> ### Name: revgeo
> ### Title: Reverse Geocoding with the Photon Geocoder for OpenStreetMap,
> ###   Google Maps, and Bing.
> ### Aliases: revgeo
> ### Keywords: geocode reverse
> 
> ### ** Examples
> 
> revgeo(longitude=-77.0229529, latitude=38.89283435)
[1] "Getting geocode data from Photon: http://photon.komoot.de/reverse?lon=-77.0229529&lat=38.89283435"

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning 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 object is masked from 'package:kableExtra':

    group_rows

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
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning 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 object is masked from 'package:kableExtra':

    group_rows

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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘RGCxGC-Ex.R’ failed
The error most likely occurred in:

> ### Name: baseline_corr
> ### Title: Bidimensional baseline correction
> ### Aliases: baseline_corr
> 
> ### ** Examples
> 
> library(colorRamps)
> chrom_name <- system.file("extdata", "08GB.cdf", package = "RGCxGC")
> chrom_2D <- read_chrom(chrom_name, 5L)
Error in RNetCDF::open.nc(object@name) : NetCDF: HDF error
Calls: read_chrom ... anyStrings -> isTRUE -> validityMethod -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Explanation.Rmd’ using rmarkdown
Warning 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 (Explanation.Rmd) 
Error: processing vignette 'Explanation.Rmd' failed with diagnostics:
NetCDF: HDF error
--- failed re-building ‘Explanation.Rmd’

SUMMARY: processing the following file failed:
  ‘Explanation.Rmd’

Error: Vignette re-building failed.
Execution halted
Package unavailable to check Rd xrefs: ‘Rsymphony’
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    doc     3.7Mb
    fonts   1.6Mb
    libs    1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
Warning 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 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'playwith', 'pmg', 'rggobi', 'SVGAnnotation'
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    extra  10.2Mb
Package required but not available: ‘RPostgres’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  atkClasses.c:1054:25: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1062:34: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  atkClasses.c:1401:51: warning: passing argument 2 of ‘object_class->active_descendant_changed’ from incompatible pointer type [-Wincompatible-pointer-types]
  gdkFuncs.c:6000:36: warning: passing argument 2 of ‘gdk_window_get_user_data’ from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1974:17: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gioClasses.c:1990:20: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:8831:28: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
  gtkClasses.c:11314:21: warning: assignment from incompatible pointer type [-Wincompatible-pointer-types]
See ‘/home/ripley/R/packages/tests32/RGtk2.Rcheck/00install.out’ for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    help  10.6Mb
    libs   3.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc          10.2Mb
    htmlwidgets   1.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘intro_rhandsontable.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_rhandsontable.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘rinatVignette.Rmd’ using rmarkdown
Warning 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 100-102 (rinatVignette.Rmd) 
Error: processing vignette 'rinatVignette.Rmd' failed with diagnostics:
cannot open the connection to 'http://www.inaturalist.org/observations/project/597.csv?page=1&per_page=100'
--- failed re-building ‘rinatVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘rinatVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
Note: information on .o files is not available
File ‘/home/ripley/R/Lib32/rJava/libs/rJava.so’:
  Found ‘exit’, possibly from ‘exit’ (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.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.0Mb
installed size is 11.2Mb
  sub-directories of 1Mb or more:
    java  11.2Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    data      1.0Mb
    extdata   3.1Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    rmd   8.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    java   4.4Mb
Running examples in ‘rmdfiltr-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_lua_filter
> ### Title: Add filter to pandoc arguments
> ### Aliases: add_lua_filter add_wordcount_filter
> ###   add_replace_ampersands_filter add_citeproc_filter add_custom_filter
> 
> ### ** Examples
> 
> 
> add_lua_filter(NULL, "wordcount", report = "silent")
Error in if (is.na(b)) return(1L) : argument is of length zero
Calls: add_lua_filter ... add_custom_filter -> verify_pandoc_version -> <Anonymous>
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rmdfiltr)
  > 
  > test_check("rmdfiltr")
  ── 1. Error: Convenience functions (@test_convenience_functions.R#4)  ──────────
  argument is of length zero
  Backtrace:
   1. testthat::expect_identical(...)
   4. rmdfiltr::add_lua_filter(filter_name = "wordcount", report = "silent")
   5. rmdfiltr::add_custom_filter(...)
   6. rmdfiltr::verify_pandoc_version(report = report)
   7. utils::compareVersion("2.0", as.character(rmarkdown::pandoc_version()))
  
  ── 2. Error: Vectorization (@test_vectorization.R#4)  ──────────────────────────
  argument is of length zero
  Backtrace:
   1. testthat::expect_identical(...)
   4. rmdfiltr::add_lua_filter(...)
   5. rmdfiltr::add_custom_filter(...)
   6. rmdfiltr::verify_pandoc_version(report = report)
   7. utils::compareVersion("2.0", as.character(rmarkdown::pandoc_version()))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Convenience functions (@test_convenience_functions.R#4) 
  2. Error: Vectorization (@test_vectorization.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘replace_ampersands.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-45 (replace_ampersands.Rmd) 
Error: processing vignette 'replace_ampersands.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘replace_ampersands.Rmd’

--- re-building ‘wordcount.Rmd’ using rmarkdown
Warning 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 47-49 (wordcount.Rmd) 
Error: processing vignette 'wordcount.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘wordcount.Rmd’

SUMMARY: processing the following files failed:
  ‘replace_ampersands.Rmd’ ‘wordcount.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    java  12.7Mb
Running examples in ‘RNetCDF-Ex.R’ failed
The error most likely occurred in:

> ### Name: create.nc
> ### Title: Create a NetCDF Dataset
> ### Aliases: create.nc
> ### Keywords: file
> 
> ### ** Examples
> 
> ##  Create empty NetCDF datasets with different formats
> file1 <- tempfile("create3_", fileext=".nc")
> nc <- create.nc(file1)
> close.nc(nc)
> unlink(file1)
> 
> file2 <- tempfile("create64_", fileext=".nc")
> nc2 <- create.nc(file2,format="offset64")
> close.nc(nc2)
> unlink(file2)
> 
> file3 <- tempfile("create4_", fileext=".nc")
> nc3 <- create.nc(file3,format="netcdf4")
Error in create.nc(file3, format = "netcdf4") : Permission denied
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.9Mb
    doc    1.7Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R  11.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘robin.Rmd’ using rmarkdown
Warning 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

Loading required package: gprege
Loading required package: gptk
Loading required package: Matrix
Loading required package: fields
Loading required package: spam
Loading required package: dotCall64
Loading required package: grid
Spam version 2.4-0 (2019-11-01) is loaded.
Type 'help( Spam)' or 'demo( spam)' for a short introduction 
and overview of this package.
Help for individual functions is also obtained by adding the
suffix '.spam' to the function name, e.g. 'help( chol.spam)'.

Attaching package: 'spam'

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

    det

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

    backsolve, forwardsolve

Loading required package: maps
See https://github.com/NCAR/Fields for
 an extensive vignette, other supplements and source code 
Quitting from lines 66-67 (robin.Rmd) 
Error: processing vignette 'robin.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘robin.Rmd’

SUMMARY: processing the following file failed:
  ‘robin.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'illuminaHumanv3.db'
Running examples in ‘RobStatTM-Ex.R’ failed
The error most likely occurred in:

> ### Name: lmrobdet.control
> ### Title: Tuning parameters for lmrobdetMM and lmrobdetDCML
> ### Aliases: lmrobdet.control
> 
> ### ** Examples
> 
> data(coleman, package='robustbase')
> m2 <- lmrobdetMM(Y ~ ., data=coleman, control=lmrobdet.control(refine.PY=50))

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

Traceback:
 1: pyinit::pyinit(x = X, y = y, intercept = FALSE, delta = dee,     cc = 1.54764, psc_keep = control$psc_keep * (1 - (p/n)),     resid_keep_method = control$resid_keep_method, resid_keep_thresh = control$resid_keep_thresh,     resid_keep_prop = control$resid_keep_prop, maxit = control$py_maxit,     eps = control$py_eps, mscale_maxit = control$mscale_maxit,     mscale_tol = control$mscale_tol, mscale_rho_fun = "bisquare")
 2: MMPY(X = x, y = y, control = control, mf = mf)
 3: lmrobdetMM(Y ~ ., data = coleman, control = lmrobdet.control(refine.PY = 50))
An irrecoverable exception occurred. R is aborting now ...
Running examples in ‘robust-Ex.R’ failed
The error most likely occurred in:

> ### Name: overlaidDenPlot.fdfm
> ### Title: Overlaid Density Plot
> ### Aliases: overlaidDenPlot.fdfm
> ### Keywords: hplot
> 
> ### ** Examples
> 
>   data(los, package="robustbase")
>   los.fm <- fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"),
+                          x = los, densfun = "gamma")

 *** caught segfault ***
address 10, cause 'memory not mapped'

Traceback:
 1: Tabgamma(b1, b2, alpha1, alpha2, k, A, maxta, maxtc, maxit, til,     tol)
 2: gammaRob(x, ...)
 3: fitdstnRob(x = los, densfun = "gamma")
 4: eval(model.call, sys.parent())
 5: eval(model.call, sys.parent())
 6: fit.models(c(Robust = "fitdstnRob", MLE = "fitdstn"), x = los,     densfun = "gamma")
An irrecoverable exception occurred. R is aborting now ...
Installation failed.
See ‘/home/ripley/R/packages/tests32/rocTree.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    R         2.8Mb
    extdata   2.8Mb
Running examples in ‘rosr-Ex.R’ failed
The error most likely occurred in:

> ### Name: create_eq
> ### Title: Create a demo equation sheet
> ### Aliases: create_eq
> 
> ### ** Examples
> 
> create_eq(tempdir())
Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/rpg.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘rpivotTableIntroduction.Rmd’

SUMMARY: processing the following file failed:
  ‘rpivotTableIntroduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/ripley/R/packages/tests32/RPostgres.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    extdata   4.9Mb
Running examples in ‘rrcovHD-Ex.R’ failed
The error most likely occurred in:

> ### Name: SosDiscRobust
> ### Title: Robust and sparse multigroup classification by the optimal
> ###   scoring approach
> ### Aliases: SosDiscRobust SosDiscRobust.default SosDiscRobust.formula
> ### Keywords: robust multivariate classification sparse
> 
> ### ** Examples
> 
> 
> ## EXAMPLE 1 ######################################
> data(olitos)
> grind <- which(colnames(olitos)=="grp")
> 
> set.seed(5008642)
> mod <- SosDiscRobust(grp~., data=olitos, lambda=0.3, maxIte=30, Q=3, tol=1e-2)
Error in callBackend("R_sparseSubsets", R_x = x, R_y = y, R_lambda = lambda,  : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: SosDiscRobust ... sparseLTS.default -> fastSparseLTS -> sparseSubsets -> callBackend
Execution halted
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(rsconnect)
  > 
  > test_check("rsconnect")
  
  ── 1. Error: simple http GET works (@test-http.R#87)  ──────────────────────────
  Operation was aborted by an application callback
  Backtrace:
   1. rsconnect:::GET(...)
   2. rsconnect:::httpRequest(...)
   3. rsconnect:::httpInvokeRequest(..., http = httpFunction())
   4. rsconnect:::http(...)
   6. base::tryCatch(...)
   7. base:::tryCatchList(expr, classes, parentenv, handlers)
   8. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   9. value[[3L]](cond)
Found the following executable file:
  data/GH.RData
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/home/ripley/R/packages/tests32/Rserve.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    libs   3.2Mb
Running ‘rsolr_unit_tests.R’ [1m/180m]
Running the tests in ‘tests/rsolr_unit_tests.R’ failed.
Complete output:
  > rsolr:::.test()
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  Solr started at: http://localhost:8983/solr/techproducts
  
  Attaching package: 'BiocGenerics'
  
  The following objects are masked from 'package:parallel':
  
      clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
      clusterExport, clusterMap, parApply, parCapply, parLapply,
      parLapplyLB, parRapply, parSapply, parSapplyLB
  
  The following objects are masked from 'package:stats':
  
      IQR, mad, sd, var, xtabs
  
  The following objects are masked from 'package:base':
  
      Filter, Find, Map, Position, Reduce, anyDuplicated, append,
      as.data.frame, basename, cbind, colnames, dirname, do.call,
      duplicated, eval, evalq, get, grep, grepl, intersect, is.unsorted,
      lapply, mapply, match, mget, order, paste, pmax, pmax.int, pmin,
      pmin.int, rank, rbind, rownames, sapply, setdiff, sort, table,
      tapply, union, unique, unsplit, which, which.max, which.min
  
  
  Attaching package: 'rsolr'
  
  The following object is masked from 'package:stats':
  
      ftable
  
  The following object is masked from 'package:base':
  
      grouping
  
  Starting Solr...
  Use options(verbose=TRUE) to diagnose any problems.
  
  Timing stopped at: 30.06 6.868 1.077e+04
  Error in file() : cannot open the connection
  Calls: <Anonymous> -> <Anonymous> -> <Anonymous> -> portIsOpen -> file
  In addition: Warning message:
  In file() :
    cannot open file '/tmp/RtmprfaWW1/working_dir/RtmpqPa4Wl/Rf1787f746511': Too many open files
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using Sweave
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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

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

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

    IQR, mad, sd, var, xtabs

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

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


Attaching package: ‘rsolr’

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

    ftable

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

    grouping


Error: processing vignette 'intro.Rnw' failed with diagnostics:
 chunk 3 (label = SolrFrame) 
Error in value[[3L]](cond) : Failed to retrieve schema.
rsolr requires schema via REST or as XML from admin module.
Error from REST: Error: Not Found



--- failed re-building ‘intro.Rnw’

SUMMARY: processing the following file failed:
  ‘intro.Rnw’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [30m/31m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > library(testthat)
  > library(rsparse)
  > library(data.table)
  > library(Matrix)
  > options(rsparse_omp_threads = 1L)
  > logger = lgr::get_logger('rsparse')
  > logger$set_threshold('warn')
  > data("movielens100k")
  > test_check("rsparse")
installed size is 14.3Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    doc    1.1Mb
    libs  10.9Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs        7.5Mb
    unitTests   1.0Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Running examples in ‘RSuite-Ex.R’ failed
The error most likely occurred in:

> ### Name: prj_pack
> ### Title: Prepares project source pack tagged with version.
> ### Aliases: prj_pack
> 
> ### ** Examples
> 
> # create exemplary project base folder
> prj_base <- tempfile("example_")
> dir.create(prj_base, recursive = TRUE, showWarnings = FALSE)
> 
> # start project
> prj <- prj_start("my_project", skip_rc = TRUE, path = prj_base)
2019-11-22 16:22:13 INFO:rsuite:Project my_project has structure compliant with current version of RSuite(v0.37.253).
2019-11-22 16:22:13 INFO:rsuite:Project my_project started.
> 
> # create package in the project
> prj_start_package("mypackage", prj = prj, skip_rc = TRUE)
2019-11-22 16:22:13 INFO:rsuite:Package mypackage started in project my_project.
> 
> # build project source pack
> pack_fpath <- prj_pack(prj = prj, path = tempdir(), pack_ver = "1.0")
2019-11-22 16:22:13 WARNING:rsuite:Project environment is not locked!
2019-11-22 16:22:13 INFO:rsuite:Exporting project from /tmp/RtmpffaGWL/working_dir/RtmpJ2aWBb/example_2de3d381b51/my_project ...
2019-11-22 16:22:13 INFO:rsuite:Exporting project from /tmp/RtmpffaGWL/working_dir/RtmpJ2aWBb/example_2de3d381b51/my_project ... done
2019-11-22 16:22:14 WARNING:rsuite:Zip building aborted for /tmp/RtmpffaGWL/working_dir/RtmpJ2aWBb/prjpack_my_project_1.0x.zip
2019-11-22 16:22:14 ERROR:rsuite:Failed to create pack file (zip returned non 0 return status).
Error: Failed to create pack file (zip returned non 0 return status).
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘rtrek.Rmd’ using rmarkdown
Warning 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 block_exec(params) :
  Failed to tidy R code in chunk 'pkg_data'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'stBooksWiki'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'st_books_wiki'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'st_books_wiki2'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'stBooks'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'stSeries'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'stTiles'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'stGeo'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Warning in block_exec(params) :
  Failed to tidy R code in chunk 'tile_coords'. Reason:
Error in loadNamespace(name) : there is no package called 'formatR'

Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘rtrek.Rmd’

SUMMARY: processing the following file failed:
  ‘rtrek.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc    7.9Mb
    libs   2.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     3.1Mb
    doc   1.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc   4.8Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    include   5.5Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      3.0Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/s2.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘R-versus-CPP.Rmd’ using rmarkdown
Warning 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 63-72 (R-versus-CPP.Rmd) 
Error: processing vignette 'R-versus-CPP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘R-versus-CPP.Rmd’

SUMMARY: processing the following file failed:
  ‘R-versus-CPP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    help   3.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sankeywheel.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 43-44 (sankeywheel.Rmd) 
Error: processing vignette 'sankeywheel.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sankeywheel.Rmd’

SUMMARY: processing the following file failed:
  ‘sankeywheel.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘sass.Rmd’

SUMMARY: processing the following file failed:
  ‘sass.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc       1.4Mb
    example   2.7Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   6.8Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data            1.5Mb
    vignette_data   2.1Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R   7.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   4.1Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc    6.3Mb
    libs   1.0Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data        1.7Mb
    sequences   2.1Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   4.1Mb
    vcf    1.0Mb
Running examples in ‘seqminer-Ex.R’ failed
The error most likely occurred in:

> ### Name: annotateGene
> ### Title: Annotate a test variant
> ### Aliases: annotateGene
> 
> ### ** Examples
> 
> if (.Platform$endian == "little") {
+   param <- list(reference = system.file("tabanno/test.fa", package = "seqminer"),
+                 geneFile = system.file("tabanno/test.gene.txt", package = "seqminer"))
+   param <- makeAnnotationParameter(param)
+   print(param)
+   annotateGene(param, c("1", "1"), c(3, 5) , c("A", "C"), c("G", "C"))
+ } else {
+   message("Tabix does not work well for big endian for now")
+ }
$reference
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.fa"

$geneFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt"

$geneFileFormat
[1] "refFlat"

$codonFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/codon.txt"

$priorityFile
[1] "/home/ripley/R/Lib32/seqminer/tabanno/priority.txt"

$upstreamRange
[1] 50

$downstreamRange
[1] 50

$spliceIntoExon
[1] 3

$spliceIntoIntron
[1] 8

$bed
NULL

$genomeScore
NULL

$tabix
NULL

$indexOutput
[1] FALSE

$inputFormat
[1] "vcf"

$checkReference
[1] TRUE

Load reference genome /home/ripley/R/Lib32/seqminer/tabanno/test.fa...
DONE: 1 chromosomes and 74 bases are loaded.
Load codon file /home/ripley/R/Lib32/seqminer/tabanno/codon.txt...
DONE: codon file loaded.
Load priority file /home/ripley/R/Lib32/seqminer/tabanno/priority.txt...
DONE: 25 priority annotation types loaded.
Load gene file /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt...
DONE: 3 gene loaded from /home/ripley/R/Lib32/seqminer/tabanno/test.gene.txt.

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

Traceback:
 1: annotateGene(param, c("1", "1"), c(3, 5), c("A", "C"), c("G",     "C"))
An irrecoverable exception occurred. R is aborting now ...
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   1.3Mb
Running examples in ‘SetMethods-Ex.R’ failed
The error most likely occurred in:

> ### Name: LR.intersect
> ### Title: Function for identifying contradictory simplifying assumptions
> ###   or easy counterfactuals.
> ### Aliases: LR.intersect
> ### Keywords: QCA
> 
> ### ** Examples
> 
> # Import your data. For example:
> 
> data(SCHF)
> 
> # Get the parsimonious solution:
> 
> sol_yp <- minimize(SCHF, outcome = "EXPORT",
+                 conditions = c("EMP","BARGAIN","UNI","OCCUP","STOCK", "MA"),
+                 incl.cut = .9, 
+                 include = "?", 					   
+                 details = TRUE, show.cases = TRUE)

 *** caught segfault ***
address fa88af00, cause 'memory not mapped'

Traceback:
 1: minimize(SCHF, outcome = "EXPORT", conditions = c("EMP", "BARGAIN",     "UNI", "OCCUP", "STOCK", "MA"), incl.cut = 0.9, include = "?",     details = TRUE, show.cases = TRUE)
An irrecoverable exception occurred. R is aborting now ...
Packages required but not available: 'RcppAnnoy', 'uwot'

Packages suggested but not available for checking: 'loomR', 'monocle'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc     12.4Mb
    sqlite   1.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘sf1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   7.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGPdata.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-28 (SGPdata.Rmd) 
Error: processing vignette 'SGPdata.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGPdata.Rmd’

SUMMARY: processing the following file failed:
  ‘SGPdata.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   3.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘sharpshootR-Ex.R’ failed
The error most likely occurred in:

> ### Name: LL2PLSS
> ### Title: PLSS2LL
> ### Aliases: LL2PLSS plssMeridians d4
> ### Keywords: manip
> 
> ### ** Examples
> 
> library(sp)
> 
> # create coordinates
> x <- -115.3823 
> y <- 48.88228
> 
> # fetch PLSS geometry for these coordinates
> p.plss <- LL2PLSS(x, y)
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘coordinates’ for signature ‘"NULL"’
Calls: LL2PLSS ... Polygons -> stopifnot -> Polygon -> coordinates -> <Anonymous>
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    www   7.6Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    www   9.1Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning 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:
there is no package called 'webshot'
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘sigminer.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
stdin: not in compressed format
Quitting from lines 59-61 (sigminer.Rmd) 
Error: processing vignette 'sigminer.Rmd' failed with diagnostics:
missing required fields from MAF: Hugo_Symbol
--- failed re-building ‘sigminer.Rmd’

SUMMARY: processing the following file failed:
  ‘sigminer.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘GeneralizedModels_legacy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘GeneralizedModels_legacy.Rmd’

--- re-building ‘Intro_legacy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Intro_legacy.Rmd’

--- re-building ‘Power_legacy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Power_legacy.Rmd) 
Error: processing vignette 'Power_legacy.Rmd' failed with diagnostics:
`levels.vctrs_list_of()` not supported.
--- failed re-building ‘Power_legacy.Rmd’

--- re-building ‘simulation_arguments.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘simulation_arguments.Rmd’

--- re-building ‘tidy_simulation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tidy_simulation.Rmd’

--- re-building ‘unbalanced_legacy.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘unbalanced_legacy.Rmd’

SUMMARY: processing the following file failed:
  ‘Power_legacy.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    doc    2.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘skm-vignettes.Rmd’ using rmarkdown
Warning 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: magrittr
Loading required package: data.table
skm_mls: skm solver via skm_mls_cpp ...

skm_mls: auto_create g w.r.t first letter of s_name.

skm_mls: optimizing on k <1> ...

skm_mls: optimizing on k <1> ... done.

skm_mls: optimizing on k <2> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <2> ... done.

skm_mls: optimizing on k <3> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <3> ... done.

skm_mls: optimizing on k <4> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <4> ... done.

skm_mls: optimizing on k <5> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <5> ... done.

skm_mls: optimizing on k <6> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <6> ... done.

skm_mls: optimizing on k <7> ...

skm_mls: set extra runs based on previous optim s ...

skm_mls: set extra runs based on previous optim s ... done.

skm_mls: optimizing on k <7> ... done.

skm_mls: optimizing on k <8> ...
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   4.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   4.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basics.Rmd’

--- re-building ‘iframes.Rmd’ using rmarkdown
Warning 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 76-87 (iframes.Rmd) 
Error: processing vignette 'iframes.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘iframes.Rmd’

--- re-building ‘pdfs.Rmd’ using rmarkdown
Warning 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 31-33 (pdfs.Rmd) 
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘pdfs.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
Warning 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 88-93 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘plots.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘iframes.Rmd’ ‘pdfs.Rmd’ ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CustomTable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘CustomTable.Rmd’

--- re-building ‘SmartEDA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 132-133 (SmartEDA.Rmd) 
Error: processing vignette 'SmartEDA.Rmd' failed with diagnostics:
unused argument (options = options)
--- failed re-building ‘SmartEDA.Rmd’

SUMMARY: processing the following file failed:
  ‘SmartEDA.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.0Mb
    doc   2.8Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    data  11.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    doc    1.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning 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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 2.97 secs
Identifing all possible orderings..
Total run time: 1.3 secs
Quitting from lines 346-347 (SourceSet.Rmd) 
Error: processing vignette 'SourceSet.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
Running ‘lint.R’
  Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > 
  > library("testthat")
  > library("spacyr")
  > 
  > test_check("spacyr")
  ── 1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.
  error in running command: 'Illegal seek'
  Backtrace:
   1. global::skip_if_no_python_or_no_spacy()
   2. spacyr::find_spacy(ask = FALSE)
   3. spacyr:::check_spacy_model(py_exec, model)
   6. base::system2(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 51 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: spacy_parse handles numbers/tibbles correctly (@test-2-spacy_parse.R#165) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-30 (intro_sparkline.Rmd) 
Error: processing vignette 'intro_sparkline.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘intro_sparkline.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_sparkline.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    java   2.5Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      5.4Mb
    doc    5.1Mb
    help   5.3Mb
    libs   1.5Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data     2.6Mb
    shapes   3.9Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc   3.6Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   2.9Mb
Installation failed.
See ‘/home/ripley/R/packages/tests32/sptm.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [15s/17s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /home/ripley/R/Lib32/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/RtmpTtaiUQ/working_dir/RtmpstaiRY/file65599a3740
  ── 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    lsndata   2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stacomir.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 281-303 (stacomir.Rmd) 
Error: processing vignette 'stacomir.Rmd' failed with diagnostics:
round(sum(datasub$value, na.rm = TRUE), 2) and round(sum(datasub2$value, na.rm = TRUE), 2) are not equal:
  Mean relative difference: 0.000996741
--- failed re-building ‘stacomir.Rmd’

SUMMARY: processing the following file failed:
  ‘stacomir.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    include   6.5Mb
    lib       1.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_analysis_of_DOM_samples.Rmd’ using rmarkdown
Warning 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

Server error [504] for doi "10.1039/c3ay41160e", you may want to try again, or BibTeX unavailable for this doi
no results with relavency score greater than 'min.relevance' successfully retrieved
Quitting from lines 25-71 (Basic_analysis_of_DOM_samples.Rmd) 
Error: processing vignette 'Basic_analysis_of_DOM_samples.Rmd' failed with diagnostics:
argument "bibtype" is missing, with no default
--- failed re-building ‘Basic_analysis_of_DOM_samples.Rmd’

--- re-building ‘PARAFAC_analysis_of_EEM.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Server error [504] for doi "10.1016/0043-1354(72)90017-6", you may want to try again, or BibTeX unavailable for this doi
no results with relavency score greater than 'min.relevance' successfully retrieved
Quitting from lines 35-63 (PARAFAC_analysis_of_EEM.Rmd) 
Error: processing vignette 'PARAFAC_analysis_of_EEM.Rmd' failed with diagnostics:
argument "bibtype" is missing, with no default
--- failed re-building ‘PARAFAC_analysis_of_EEM.Rmd’

SUMMARY: processing the following files failed:
  ‘Basic_analysis_of_DOM_samples.Rmd’ ‘PARAFAC_analysis_of_EEM.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc       1.3Mb
    extdata   5.5Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    doc  10.6Mb
    nc    4.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R          2.3Mb
    datasets   2.7Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    libs  33.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 61-64 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
Process terminated
--- failed re-building ‘stRvignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stRvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.5Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    doc    2.8Mb
    help   1.0Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    data   3.3Mb
    doc    3.9Mb
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    data  12.2Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc   5.3Mb
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.
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    extdata   4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R         1.3Mb
    extdata   3.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc   6.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘HTML.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
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

--- finished re-building ‘tables.Rnw’

SUMMARY: processing the following file failed:
  ‘HTML.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    java  11.5Mb
Running ‘testthat.R’ [46s/159s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  ── 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  ───────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc           1.9Mb
    simulations   3.1Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    doc    3.9Mb
Packages suggested but not available for checking:
  'lpsymphony', 'Rsymphony', 'gurobi'
Running examples in ‘texPreview-Ex.R’ failed
The error most likely occurred in:

> ### Name: as.kable
> ### Title: Try to coerce an object into a knitr_kable object
> ### Aliases: as.kable
> 
> ### ** Examples
> 
> 
> tex <- '\\begin{tabular}{llr}
+ \\hline
+ \\multicolumn{2}{c}{Item} \\\\
+ \\cline{1-2}
+ Animal    & Description & Price (\\$) \\\\
+ \\hline
+ Gnat      & per gram    & 13.65      \\\\
+ & each        & 0.01       \\\\
+ Gnu       & stuffed     & 92.50      \\\\
+ Emu       & stuffed     & 33.33      \\\\
+ Armadillo & frozen      & 8.99       \\\\
+ \\hline
+ \\end{tabular}'
> 
> ktex <- as.kable(tex)
> 
> class(ktex)
[1] "knitr_kable"
> 
> attributes(ktex)
$class
[1] "knitr_kable"

$format
[1] "latex"

> 
> ktex
\begin{tabular}{llr}
\hline
\multicolumn{2}{c}{Item} \\
\cline{1-2}
Animal    & Description & Price (\$) \\
\hline
Gnat      & per gram    & 13.65      \\
& each        & 0.01       \\
Gnu       & stuffed     & 92.50      \\
Emu       & stuffed     & 33.33      \\
Armadillo & frozen      & 8.99       \\
\hline
\end{tabular}
> 
> # using an input call
> 
> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, keep_pdf,  : 
   
! LaTeX Error: File `/tmp/RtmpGXay_o/working_dir/RtmpaIaGiu/tex_temp.tex ' not 
found.

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

Enter file name: 
! Emergency stop.
<read *> 
 
l.17 ...ay_o/working_dir/RtmpaIaGiu/tex_temp.tex }
 ^^M 
!  ==> Fatal error occurred, no output PDF file produced!
Calls: tex_preview -> tex_preview.character -> tex_preview.default
Execution halted
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    doc    3.8Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    data   8.6Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    rda    7.7Mb
Running examples in ‘tidync-Ex.R’ failed
The error most likely occurred in:

> ### Name: hyper_array
> ### Title: Extract NetCDF data as an array
> ### Aliases: hyper_array tidync_data hyper_slice hyper_array.tidync
> ###   hyper_array.character
> 
> ### ** Examples
> 
> f <- "S20080012008031.L3m_MO_CHL_chlor_a_9km.nc"
> l3file <- system.file("extdata/oceandata", f, package= "tidync")
> 
> ## extract a raw list by filtered dimension
> 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

> araw1 <- tidync(l3file) %>%
+  hyper_filter(lat = between(lat, -78, -75.8), 
+               lon = between(lon, 165, 171)) %>%
+  hyper_array()
Error in RNetCDF::open.nc(x) : NetCDF: HDF error
Calls: %>% -> eval -> eval -> tidync -> tidync.character
Execution halted
Package suggested but not available for checking: ‘Rblpapi’
Package unavailable to check Rd xrefs: ‘Rblpapi’
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc       1.5Mb
    extdata   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
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'
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘tiler.Rmd’ using rmarkdown
Warning 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
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tilesIMG.py", line 47, in <module>
    import gdal
ImportError: No module named gdal
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tiles.py", line 52, in <module>
    from osgeo import gdal
ImportError: No module named osgeo
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tilesIMG.py", line 47, in <module>
    import gdal
ImportError: No module named gdal
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tiles.py", line 52, in <module>
    from osgeo import gdal
ImportError: No module named osgeo
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tilesIMG.py", line 47, in <module>
    import gdal
ImportError: No module named gdal
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tiles.py", line 52, in <module>
    from osgeo import gdal
ImportError: No module named osgeo
Traceback (most recent call last):
  File "/home/ripley/R/Lib32/tiler/python/gdal2tilesIMG.py", line 47, in <module>
    import gdal
ImportError: No module named gdal
Quitting from lines 208-214 (tiler.Rmd) 
Error: processing vignette 'tiler.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘tiler.Rmd’

SUMMARY: processing the following file failed:
  ‘tiler.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘dbarts’
Error(s) in re-building vignettes:
  ...
--- re-building ‘toOrdinal.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘toOrdinal.Rmd’

SUMMARY: processing the following file failed:
  ‘toOrdinal.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    doc   4.0Mb
Package suggested but not available for checking: ‘moveVis’
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   5.3Mb
Package unavailable to check Rd xrefs: ‘moveVis’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    doc    2.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
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 sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    fonts   5.3Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    doc    4.3Mb
    libs   7.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning 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'
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
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 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: Rosenbrock (@test_rosenbrock.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘TSplotly.Rmd’ using rmarkdown
Warning 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: TSplotly
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Loading required package: plotly

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: forecast
Quitting from lines 99-117 (TSplotly.Rmd) 
Error: processing vignette 'TSplotly.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘TSplotly.Rmd’

SUMMARY: processing the following file failed:
  ‘TSplotly.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc     1.5Mb
    fonts   2.9Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    doc     6.7Mb
    ubinc   2.1Mb
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc         7.3Mb
    dummydata   1.5Mb
    libs        1.9Mb
Package suggested but not available for checking: ‘TSstudio’
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    data   3.9Mb
    doc    8.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘UKgrid_vignette.Rmd’ using rmarkdown
Warning 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'
--- failed re-building ‘UKgrid_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘UKgrid_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    help   4.1Mb
Running examples in ‘umx-Ex.R’ failed
The error most likely occurred in:

> ### Name: RMSEA.summary.mxmodel
> ### Title: RMSEA function for MxModels
> ### Aliases: RMSEA.summary.mxmodel
> 
> ### ** Examples
> 
> require(umx)
> data(demoOneFactor)
> manifests = names(demoOneFactor)
> 
> m1 = umxRAM("One Factor", data = demoOneFactor, type = "cov",
+ 	umxPath("G", to = manifests),
+ 	umxPath(var = manifests),
+ 	umxPath(var = "G", fixedAt = 1.0)
+ )
A latent variable 'G' was created. 
Running One Factor with 10 parameters

 *** caught segfault ***
address 7, cause 'memory not mapped'
Running ‘testthat.R’ [0m/180m]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(umx)
  Loading required package: OpenMx
  To take full advantage of multiple cores, use:
    mxOption(key='Number of Threads', value=parallel::detectCores()) #now
    Sys.setenv(OMP_NUM_THREADS=parallel::detectCores()) #before library(OpenMx)
  For an overview type '?umx'
  
  Attaching package: 'umx'
  
  The following object is masked from 'package:stats':
  
      loadings
  
  > 
  > test_check("umx")
  
   *** caught segfault ***
  address b02b0550, cause 'memory not mapped'
Error(s) in re-building vignettes:
  ...
--- re-building ‘convexhull.Rmd’ using rmarkdown
Warning 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 93-98 (convexhull.Rmd) 
Error: processing vignette 'convexhull.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘convexhull.Rmd’

SUMMARY: processing the following file failed:
  ‘convexhull.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    doc   1.9Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    doc   7.8Mb
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  8.8Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   6.6Mb
Package required but not available: ‘RcppAnnoy’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘varrank.Rmd’ using knitr
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'
--- failed re-building ‘varrank.Rmd’

SUMMARY: processing the following file failed:
  ‘varrank.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning 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 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘basic_usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_to_vegalite.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘intro_to_vegalite.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_to_vegalite.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    R   2.8Mb
installed size is  9.4Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    1.3Mb
    help   3.0Mb
Running examples in ‘virtuoso-Ex.R’ failed
The error most likely occurred in:

> ### Name: vos_connect
> ### Title: Connect to a Virtuoso Server over ODBC
> ### Aliases: vos_connect
> 
> ### ** Examples
> 
> vos_status()
Error in ps_pids() : Not implemented for this platform
Calls: vos_status ... vos_process -> virtuoso_pid -> <Anonymous> -> ps_pids
Execution halted
Running ‘spelling.R’
  Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(virtuoso)
  > 
  > Sys.setenv(INTERACTIVE = FALSE) # Overrides detected interactive behavior
  > test_check("virtuoso")
  ── 1. Error: assert allowed dirs exits if server not connected  (@test-utilities
  Not implemented for this platform
  Backtrace:
   1. testthat::skip_if(!is.null(suppressMessages(vos_status())))
   5. virtuoso::vos_status()
   6. virtuoso::vos_process(p)
   7. virtuoso:::virtuoso_pid()
   8. ps::ps(...)
   9. ps::ps_pids()
  
  ── 2. Error: We can generate an odbcinst file (@test-vos_odbc.R#19)  ───────────
  EXPR must be a length 1 vector
  Backtrace:
   1. virtuoso:::vos_odbcinst()
   5. virtuoso:::find_odbc_driver()
  
  Error in ps_pids() : Not implemented for this platform
  ── 3. Error: vos_process errors when not cached (@test-without-vos.R#4)  ───────
  Not implemented for this platform
  Backtrace:
   1. base::suppressMessages(vos_kill())
   3. virtuoso::vos_kill()
   4. virtuoso::vos_status(p)
   5. virtuoso::vos_process(p)
   6. virtuoso:::virtuoso_pid()
   7. ps::ps(...)
   8. ps::ps_pids()
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 10 | SKIPPED: 9 | WARNINGS: 1 | FAILED: 3 ]
  1. Error: assert allowed dirs exits if server not connected  (@test-utilities.R#16) 
  2. Error: We can generate an odbcinst file (@test-vos_odbc.R#19) 
  3. Error: vos_process errors when not cached (@test-without-vos.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   4.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-visNetwork.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Introduction-to-visNetwork.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-visNetwork.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   5.8Mb
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 12.7Mb
  sub-directories of 1Mb or more:
    doc  12.1Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    data   5.8Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    bn   7.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wordcloud.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘wordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘wordcloud.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   7.1Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    data  13.4Mb
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    data  11.9Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning 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
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

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: '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 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
there is no package called 'webshot'
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/ripley/R/packages/tests32/x13binary.Rcheck/00install.out’ for details.
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Running examples in ‘xgboost-Ex.R’ failed
The error most likely occurred in:

> ### Name: cb.gblinear.history
> ### Title: Callback closure for collecting the model coefficients history
> ###   of a gblinear booster during its training.
> ### Aliases: cb.gblinear.history
> 
> ### ** Examples
> 
> #### Binary classification:
> #
> # In the iris dataset, it is hard to linearly separate Versicolor class from the rest
> # without considering the 2nd order interactions:
> require(magrittr)
Loading required package: magrittr
> x <- model.matrix(Species ~ .^2, iris)[,-1]
> colnames(x)
 [1] "Sepal.Length"              "Sepal.Width"              
 [3] "Petal.Length"              "Petal.Width"              
 [5] "Sepal.Length:Sepal.Width"  "Sepal.Length:Petal.Length"
 [7] "Sepal.Length:Petal.Width"  "Sepal.Width:Petal.Length" 
 [9] "Sepal.Width:Petal.Width"   "Petal.Length:Petal.Width" 
> dtrain <- xgb.DMatrix(scale(x), label = 1*(iris$Species == "versicolor"))
> param <- list(booster = "gblinear", objective = "reg:logistic", eval_metric = "auc",
+               lambda = 0.0003, alpha = 0.0003, nthread = 2)
> # For 'shotgun', which is a default linear updater, using high eta values may result in
> # unstable behaviour in some datasets. With this simple dataset, however, the high learning
> # rate does not break the convergence, but allows us to illustrate the typical pattern of
> # "stochastic explosion" behaviour of this lock-free algorithm at early boosting iterations.
> bst <- xgb.train(param, dtrain, list(tr=dtrain), nrounds = 200, eta = 1.,
+                  callbacks = list(cb.gblinear.history()))
Error: segfault from C stack overflow
Execution halted
Running ‘testthat.R’
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xgboost)
  > 
  > test_check("xgboost")
  [1]	train-error:0.047136 
  Error: segfault from C stack overflow
  Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    java  19.3Mb
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    java  10.9Mb
Running ‘testthat.R’ [9s/19s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(xml2)
  > 
  > test_check("xml2")
  This is libxml2 version 2.9.9 
  terminate called after throwing an instance of 'Rcpp::exception'
    what():  Document is empty [4]
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R             1.0Mb
    exampleData   1.5Mb
    examples      4.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    doc   3.1Mb
Found the following significant warnings:
  yakmo.h:184:1: warning: ISO C++ forbids converting a string constant to ‘char*’ [-Wwrite-strings]
See ‘/home/ripley/R/packages/tests32/yakmoR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  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.
src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_FFLAGS but not SHLIB_OPENMP_CFLAGS in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_LIBS but linking is by C
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
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.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
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.
Package required but not available: ‘randomcoloR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘bibliometrix-vignette.Rmd’ using rmarkdown
Quitting from lines 268-269 (bibliometrix-vignette.Rmd) 
Error: processing vignette 'bibliometrix-vignette.Rmd' failed with diagnostics:
'to' must be a finite number
--- failed re-building ‘bibliometrix-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘bibliometrix-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
Running examples in ‘biomartr-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: getENSEMBLInfo
> ### Title: Retrieve ENSEMBL info file
> ### Aliases: getENSEMBLInfo
> 
> ### ** Examples
> 
> info.file <- getENSEMBLInfo()
Error in open.connection(con, "rb") : HTTP error 500.
Calls: getENSEMBLInfo ... parse_and_simplify -> parseJSON -> parse_con -> open -> open.connection
Execution halted
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.
Running ‘test.R’ [170s/110s]
Running the tests in ‘tests/test.R’ failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  ── 1. Error: arguments are checked (@testAnalysis.R#12)  ───────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: arguments are checked (@testData.R#532)  ──────────────────────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Running ‘test-all.R’ [28s/30s]
Running the tests in ‘tests/test-all.R’ failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  ── 1. Failure: extract au (@test-pvclust_extract.R#12)  ────────────────────────
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
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.
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.
src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_FFLAGS but not SHLIB_OPENMP_CXXFLAGS in PKG_LIBS
  src/Makevars: SHLIB_OPENMP_FFLAGS is included in PKG_LIBS but linking is by C++
Use of these macros is discussed in sect 1.2.1.1 of ‘Writing R
Extensions’. The macros for different languages may differ so the
matching macro must be used in PKG_CXXFLAGS (etc) and match that used
in PKG_LIBS (except for Fortran: see the manual).
Running examples in ‘edgarWebR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cik_search
> ### Title: SEC CIK Search
> ### Aliases: cik_search
> 
> ### ** Examples
> 
> cik_search("cloudera")
Error in read_html.response(res, base_url = href) : 
  Service Unavailable (HTTP 503).
Calls: cik_search -> <Anonymous> -> read_html.response -> <Anonymous>
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘edgarWebR.Rmd’ using rmarkdown

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 71-85 (edgarWebR.Rmd) 
Error: processing vignette 'edgarWebR.Rmd' failed with diagnostics:
Service Unavailable (HTTP 503).
--- failed re-building ‘edgarWebR.Rmd’

--- re-building ‘parsing.Rmd’ using rmarkdown
--- finished re-building ‘parsing.Rmd’

SUMMARY: processing the following file failed:
  ‘edgarWebR.Rmd’

Error: Vignette re-building failed.
Execution halted
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.
Missing or unexported object: ‘glmnet::predict.coxnet’
coef,PSP: no visible global function definition for ‘predict.coxnet’
Undefined global functions or variables:
  predict.coxnet
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiStats.Rmd’ using rmarkdown
Loading required package: epiR
Loading required package: survival
Package epiR 1.0-4 is loaded
Type help(epi.about) for summary information


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

! Missing number, treated as zero.
<to be read again> 
                   \protect 
l.136 ...nter}\rule{0.5\linewidth}{\linethickness}
                                                  \end{center} 

Error: processing vignette 'EpiStats.Rmd' failed with diagnostics:
Failed to compile EpiStats.tex. See https://yihui.name/tinytex/r/#debugging for debugging tips. See EpiStats.log for more info.
--- failed re-building ‘EpiStats.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiStats.Rmd’

Error: Vignette re-building failed.
Execution halted
Malformed Description field: should contain one or more complete sentences.
BugReports field is not a suitable URL but contains an email address
  which will be used as from R 3.4.0
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘FeatureHashing.Rmd’ using rmarkdown
Quitting from lines 68-96 (FeatureHashing.Rmd) 
Error: processing vignette 'FeatureHashing.Rmd' failed with diagnostics:
could not find function "auc"
--- failed re-building ‘FeatureHashing.Rmd’

--- re-building ‘SentimentAnalysis.Rmd’ using rmarkdown
--- finished re-building ‘SentimentAnalysis.Rmd’

SUMMARY: processing the following file failed:
  ‘FeatureHashing.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [149s/164s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  ── 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  ──────────────
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  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:
  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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘glancedata.Rmd’ using rmarkdown

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 132-153 (glancedata.Rmd) 
Error: processing vignette 'glancedata.Rmd' failed with diagnostics:
object ‘stat’ not found
--- failed re-building ‘glancedata.Rmd’

SUMMARY: processing the following file failed:
  ‘glancedata.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gqlr.Rcheck/00install.out’ for details.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/gwsem.Rcheck/00install.out’ for details.
Missing or unexported object: ‘glmnet::coef.cv.glmnet’
Running examples in ‘HCTR-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: highdim.p
> ### Title: p-values in high-dimensional linear model
> ### Aliases: highdim.p
> 
> ### ** Examples
> 
> set.seed(10)
> X <- matrix(rnorm(20000), nrow = 100)
> beta <- rep(0, 200)
> beta[1:100] <- 5
> Y <- MASS::mvrnorm(n = 1, mu = X%*%beta, Sigma = diag(100))
> result <- highdim.p(Y=Y, X=X, type = "Lasso", B = 2, fold.num = 10)
Error: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘design-principles.Rmd’ using rmarkdown
--- finished re-building ‘design-principles.Rmd’

--- re-building ‘huxreg.Rmd’ using rmarkdown
Quitting from lines 51-53 (huxreg.Rmd) 
Error: processing vignette 'huxreg.Rmd' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘huxreg.Rmd’

--- re-building ‘huxtable.Rmd’ using rmarkdown

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: 'huxtable'

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

    add_rownames

Quitting from lines 42-43 (huxtable.Rmd) 
Error: processing vignette 'huxtable.Rmd' failed with diagnostics:
Overlapping multirow/multicolumn cells in [5, 2] of huxtableOverlapping multirow/multicolumn cells in [5, 3] of huxtable
--- failed re-building ‘huxtable.Rmd’

--- re-building ‘themes.Rmd’ using rmarkdown
--- finished re-building ‘themes.Rmd’

SUMMARY: processing the following files failed:
  ‘huxreg.Rmd’ ‘huxtable.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pritikin-schmidt.Rnw’ using knitr
Killed
Running ‘testthat.R’ [127s/140s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(interactions)
  > 
  > test_check("interactions")
  ── 1. Error: as_huxtable.sim_margins works (@test_sim_margins.R#110)  ──────────
  subscript out of bounds
  Backtrace:
    1. testthat::expect_is(as_huxtable.sim_margins(ss3), "huxtable")
    4. interactions:::as_huxtable.sim_margins(ss3)
    5. interactions:::make_table(...)
    6. huxtable::insert_row(tab, c(lab, rep(NA, col_mult)), after = row)
    8. huxtable:::`colspan<-.huxtable`(`*tmp*`, value = `*vtmp*`)
    9. huxtable:::check_span_shadows(ht, "col", value)
   10. huxtable:::display_cells(ht, new_colspan = value)
  
  ── 2. Error: as_huxtable.sim_slopes works (@test_sim_slopes.R#77)  ─────────────
  subscript out of bounds
  Backtrace:
    1. testthat::expect_is(as_huxtable.sim_slopes(ss3), "huxtable")
    4. interactions:::as_huxtable.sim_slopes(ss3)
    5. interactions:::make_table(...)
    6. huxtable::insert_row(tab, c(lab, rep(NA, col_mult)), after = row)
    8. huxtable:::`colspan<-.huxtable`(`*tmp*`, value = `*vtmp*`)
    9. huxtable:::check_span_shadows(ht, "col", value)
   10. huxtable:::display_cells(ht, new_colspan = value)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 159 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: as_huxtable.sim_margins works (@test_sim_margins.R#110) 
  2. Error: as_huxtable.sim_slopes works (@test_sim_slopes.R#77) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:183:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘value_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:897:16: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} with no trivial copy-assignment; use copy-assignment or copy-initialization instead [-Wclass-memaccess]
  /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/BH/include/boost/container/detail/copy_move_algo.hpp:197:19: warning: ‘void* memmove(void*, const void*, size_t)’ writing to an object of type ‘boost::movelib::detail::iterator_to_element_ptr<boost::container::dtl::pair<int, int>*>::element_type’ {aka ‘struct boost::container::dtl::pair<int, int>’} 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/lolog.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Manifolds/SmartSpace.cpp:147:25: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/ManifoldOptim.Rcheck/00install.out’ for details.
Package required but not available: ‘symbolicDA’

See section ‘The DESCRIPTION file’ 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.
Running ‘testthat.R’ [27s/30s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(MixSIAR)
  > 
  > test_check("MixSIAR")
  ── 1. Error: Killer whale ex works  ────────────────────────────────────────────
  Error in node cross[1,1:5,3]
  Invalid parent values
  
  Backtrace:
   1. MixSIAR::run_model(...)
   2. R2jags::jags(...)
   3. rjags::jags.model(...)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Killer whale ex works 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  connection.cpp:67:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:37:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
  odbc_connection.cpp:75:36: warning: catching polymorphic type ‘class nanodbc::database_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/odbc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  opus_miner.cpp:90:15: warning: catching polymorphic type ‘class std::bad_alloc’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/opusminer.Rcheck/00install.out’ for details.
Missing or unexported objects:
  ‘glmnet::coef.cv.glmnet’ ‘glmnet::predict.cv.glmnet’
  ‘glmnet::print.glmnet’
Running examples in ‘plsmselect-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: cumbasehaz
> ### Title: Cumulative Baseline Hazard of a gamlasso object
> ### Aliases: cumbasehaz
> 
> ### ** Examples
> 
> library(plsmselect)
> library(tidyverse)
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.3
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.0.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
> 
> data(simData)
> 
> ## Fit Cox gamlasso model using the formula approach:
> ## (L1-penalty both on X terms and smooth terms (bs="ts"))
> simData$X = model.matrix(~x1+x2+x3+x4+x5+x6+x7+x8+x9+x10, data=simData)[,-1]
> 
> cfit = gamlasso(time ~ X +
+                   s(z1, bs="ts", k=5) +
+                   s(z2, bs="ts", k=5) +
+                   s(z3, bs="ts", k=5) +
+                   s(z4, bs="ts", k=5),
+                 data = simData,
+                 family = "cox",
+                 weights="status",
+                 seed=1)
Fitting a lasso and gam loop ... 

Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘plsmselect.Rmd’ using rmarkdown
── Attaching packages ─────────────────────────────────────── tidyverse 1.3.0 ──
✔ ggplot2 3.2.1     ✔ purrr   0.3.3
✔ tibble  2.1.3     ✔ dplyr   0.8.3
✔ tidyr   1.0.0     ✔ stringr 1.4.0
✔ readr   1.3.1     ✔ forcats 0.4.0
── Conflicts ────────────────────────────────────────── tidyverse_conflicts() ──
✖ dplyr::filter() masks stats::filter()
✖ dplyr::lag()    masks stats::lag()
Fitting a lasso and gam loop ... 

Quitting from lines 168-180 (plsmselect.Rmd) 
Error: processing vignette 'plsmselect.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building ‘plsmselect.Rmd’

SUMMARY: processing the following file failed:
  ‘plsmselect.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(purrrogress)
  > 
  > test_check("purrrogress")
  ── 1. Failure: R6_txt_progress (@R6_box_progress.R#264)  ───────────────────────
  `pb\$step\(\)` does not match "1000/1000 |=+|\\(100%\\) 00:00:00 remaining\n".
  Actual value: "\\n   1/1000 \|             \|\(0%\) NA remaining"
  
  ── 2. Failure: R6_line_progress (@R6_box_progress.R#358)  ──────────────────────
  pb$bar == paste0("┣", strrep("━", 18), "│") isn't true.
  
  ── 3. Error: R6_line_progress (@R6_box_progress.R#360)  ────────────────────────
  invalid format '% 2d'; use format %f, %e, %g or %a for numeric objects
  Backtrace:
    1. testthat::expect_output(pb$step())
   21. base::sprintf(format, self$current, self$total)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 280 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Failure: R6_txt_progress (@R6_box_progress.R#264) 
  2. Failure: R6_line_progress (@R6_box_progress.R#358) 
  3. Error: R6_line_progress (@R6_box_progress.R#360) 
  
  Error: testthat unit tests failed
  Execution halted
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.
Installation failed.
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/randomcoloR.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 notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/Rblpapi.Rcheck/00install.out’ for details.
Package required but not available: ‘BiBitR’

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.

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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.
Running ‘testthat.R’ [54s/57s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(recipes)
  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
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check(package = "recipes")
  ── 1. Error: quasiquotation (@test_slice.R#40)  ────────────────────────────────
  `call` must be a call
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 1394 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quasiquotation (@test_slice.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘UsingrerddapXtracto.Rmd’ using rmarkdown
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
proj_create: init=epsg:/init=IGNF: syntax not supported in non-PROJ4 emulation mode
Quitting from lines 523-533 (UsingrerddapXtracto.Rmd) 
Error: processing vignette 'UsingrerddapXtracto.Rmd' failed with diagnostics:
stopping download
--- failed re-building ‘UsingrerddapXtracto.Rmd’

SUMMARY: processing the following file failed:
  ‘UsingrerddapXtracto.Rmd’

Error: Vignette re-building failed.
Execution halted
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:
  DbResult.cpp:81:41: warning: catching polymorphic type ‘class MariaResultPrep::UnsupportedPS’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RMariaDB.Rcheck/00install.out’ for details.
Found the following significant warnings:
  nxsreader.cpp:659:22: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
  nxsreader.cpp:709:25: warning: catching polymorphic type ‘class NxsException’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/rncl.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/rphast.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/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 notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/RVowpalWabbit.Rcheck/00install.out’ for details.
Running examples in ‘RYoudaoTranslate-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: RYoudaoTranslate-package
> ### Title: R package provide functions to translate English words into
> ###   Chinese.
> ### Aliases: RYoudaoTranslate-package RYoudaoTranslate
> ### Keywords: Youdao
> 
> ### ** Examples
> 
> 	library(RCurl)
> 	library(rjson)
> 	apikey = "498375134"
> 	keyfrom = "JustForTestYouDao"
> 	youdaoLookUp("youdao",api=apikey,keyfrom=keyfrom)
Error in fromJSON(url) : unexpected character 'T'
Calls: youdaoLookUp -> youdaoDisplay -> youdaoTranslate -> fromJSON
Execution halted
Malformed Title field: should not end in a period.
BugReports field is not a suitable URL but appears to contain an email address
  not specified by mailto: nor contained in < >
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:
  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.
Running ‘testthat.R’ [14s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: /home/hornik/tmp/R.check/r-release-gcc/Work/build/Packages/SqlRender/sql/sql_server/test.sql
  Writing R function to: /tmp/RtmpI58vSf/file3a1641ecd978
  ── 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ── 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
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:
  computeQ.cpp:75:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:134:15: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
  computeQ.cpp:142:17: warning: catching polymorphic type ‘class std::runtime_error’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/strum.Rcheck/00install.out’ for details.
Found the following significant warnings:
  rapi.cc:191:12: warning: catching polymorphic type ‘struct subprocess::subprocess_exception’ by value [-Wcatch-value=]
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/subprocess.Rcheck/00install.out’ for details.
Package required but not available: ‘RSDA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [85s/62s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  WARNING: An illegal reflective access operation has occurred
  WARNING: Illegal reflective access by RJavaTools to method java.util.ArrayList$Itr.hasNext()
  WARNING: Please consider reporting this to the maintainers of RJavaTools
  WARNING: Use --illegal-access=warn to enable warnings of further illegal reflective access operations
  WARNING: All illegal access operations will be denied in a future release
  ── 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  ───────────
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Missing or unexported objects:
  ‘glmnet::coef.cv.glmnet’ ‘glmnet::predict.cv.glmnet’
Running examples in ‘TANDEM-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: coef.tandem
> ### Title: Returns the regression coefficients from a TANDEM fit
> ### Aliases: coef.tandem
> 
> ### ** Examples
> 
> # unpack example data
> x = example_data$x
> y = example_data$y
> upstream = example_data$upstream
> 
> # fit a tandem model, determine the coefficients and create a prediction
> fit = tandem(x, y, upstream, alpha=0.5)
Error: 'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘my-vignette.Rmd’ using rmarkdown
Loading required package: Matrix
Loaded glmnet 3.0-1

Quitting from lines 27-31 (my-vignette.Rmd) 
Error: processing vignette 'my-vignette.Rmd' failed with diagnostics:
'predict.cv.glmnet' is not an exported object from 'namespace:glmnet'
--- failed re-building ‘my-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘my-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘texPreview-Ex.R’ failed
The error most likely occurred in:

> base::assign(".ptime", proc.time(), pos = "CheckExEnv")
> ### Name: as.kable
> ### Title: Try to coerce an object into a knitr_kable object
> ### Aliases: as.kable
> 
> ### ** Examples
> 
> 
> tex <- '\\begin{tabular}{llr}
+ \\hline
+ \\multicolumn{2}{c}{Item} \\\\
+ \\cline{1-2}
+ Animal    & Description & Price (\\$) \\\\
+ \\hline
+ Gnat      & per gram    & 13.65      \\\\
+ & each        & 0.01       \\\\
+ Gnu       & stuffed     & 92.50      \\\\
+ Emu       & stuffed     & 33.33      \\\\
+ Armadillo & frozen      & 8.99       \\\\
+ \\hline
+ \\end{tabular}'
> 
> ktex <- as.kable(tex)
> 
> class(ktex)
[1] "knitr_kable"
> 
> attributes(ktex)
$class
[1] "knitr_kable"

$format
[1] "latex"

> 
> ktex
\begin{tabular}{llr}
\hline
\multicolumn{2}{c}{Item} \\
\cline{1-2}
Animal    & Description & Price (\$) \\
\hline
Gnat      & per gram    & 13.65      \\
& each        & 0.01       \\
Gnu       & stuffed     & 92.50      \\
Emu       & stuffed     & 33.33      \\
Armadillo & frozen      & 8.99       \\
\hline
\end{tabular}
> 
> # using an input call
> 
> x <- tex_preview(tex,returnType = 'input')
Error in tex_preview.default(obj, tex_lines, stem, overwrite, keep_pdf,  : 
   
! LaTeX Error: File `/tmp/RtmpJWsWkG/tex_temp.tex ' not found.

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

Enter file name: 
! Emergency stop.
<read *> 
 
l.17 \input{ /tmp/RtmpJWsWkG/tex_temp.tex }
 ^^M 
!  ==> Fatal error occurred, no output PDF file produced!
Calls: tex_preview -> tex_preview.character -> tex_preview.default
Execution halted
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:
  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:
  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.
Running ‘testthat.R’ [16s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(wilson)
  
  Attaching package: 'wilson'
  
  The following object is masked from 'package:stats':
  
      heatmap
  
  > 
  > test_check("wilson")
  ── 1. Error: complexHeatmap is downloadable (@test-download.R#38)  ─────────────
  getter call used outside of a complex assignment.
  Backtrace:
    1. testthat::expect_silent(...)
    9. wilson:::download(...)
   11. ComplexHeatmap::draw(plot, heatmap_legend_side = "bottom")
   12. ComplexHeatmap:::.local(object, ...)
   14. ComplexHeatmap::draw(ht_list, ...)
   15. ComplexHeatmap:::.local(object, ...)
   17. ComplexHeatmap::make_layout(...)
   18. ComplexHeatmap:::.local(object, ...)
   20. ComplexHeatmap::make_row_cluster(ht_main)
   21. ComplexHeatmap:::.local(object, ...)
   22. ComplexHeatmap:::make_cluster(object, "row")
   23. base::lapply(dend_list, adjust_dend_by_x)
   24. ComplexHeatmap:::FUN(X[[i]], ...)
   25. ComplexHeatmap:::adj_dend()
   26. ComplexHeatmap:::adj_dend(c(ind, i))
   27. ComplexHeatmap:::adj_dend(c(ind, i))
   30. base::NextMethod("[[")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 55 | SKIPPED: 5 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: complexHeatmap is downloadable (@test-download.R#38) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/home/hornik/tmp/R.check/r-release-gcc/Work/PKGS/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   3.5Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    R  35.3Mb
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs  12.9Mb
Package suggested but not available for checking: 'REBayes'
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    java   7.7Mb
Running examples in 'AWR.Kinesis-Ex.R' failed
The error occurred in:


R version 3.6.1 (2019-07-05) -- "Action of the Toes"
Copyright (C) 2019 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 <- "AWR.Kinesis"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> options(pager = "console")
> library('AWR.Kinesis')
> 
> base::assign(".oldSearch", base::search(), pos = 'CheckExEnv')
> base::assign(".old_wd", base::getwd(), pos = 'CheckExEnv')
> cleanEx()
Error: connections left open:
	stdin (file)
Execution halted
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   2.0Mb
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs   2.2Mb
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.8Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.3Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bdl.Rcheck/00install.out' for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    data   6.6Mb
installed size is 150.1Mb
  sub-directories of 1Mb or more:
    include  149.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/BiBitR.Rcheck/00install.out' for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      2.9Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs   1.5Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Cairo.Rcheck/00install.out' for details.
Error(s) in re-building vignettes:
--- re-building 'commonsMath.Rmd' using rmarkdown
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>


--- failed re-building 'commonsMath.Rmd'

SUMMARY: processing the following file failed:
  'commonsMath.Rmd'

Error: Vignette re-building failed.
Execution halted
Running 'test.R' [89s]
Running the tests in 'tests/test.R' failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  -- 1. Error: arguments are checked (@testAnalysis.R#12)  -----------------------
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  -- 2. Error: arguments are checked (@testData.R#532)  --------------------------
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  == testthat results  ===========================================================
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'Crossover-Ex.R' failed
The error most likely occurred in:

> ### Name: CrossoverDesign-class
> ### Title: Class CrossoverDesign
> ### Aliases: CrossoverDesign-class CrossoverDesign
> ###   show,CrossoverDesign-method print,CrossoverDesign-method
> ### Keywords: graphs
> 
> ### ** Examples
> 
> 
> 
> design <- t(rbind(c(1,1,2,2),
+                   c(2,2,1,1),
+                   c(1,1,2,2),
+                   c(2,2,1,1),
+                   c(1,2,2,1),
+                   c(2,1,1,2)))
>                    
> new("CrossoverDesign", design)
 (s=6, p=4, v=2)
     [,1] [,2] [,3] [,4] [,5] [,6]
[1,]    1    2    1    2    1    2
[2,]    1    2    1    2    2    1
[3,]    2    1    2    1    2    1
[4,]    2    1    2    1    1    2

Error in rcd(design, v = v, model = model) : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: <Anonymous> ... <Anonymous> -> cat -> design.efficiency -> estimable -> rcd
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/CRPClustering.Rcheck/00install.out' for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/CSFA.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DBHC.Rcheck/00install.out' for details.
Running examples in 'DCD-Ex.R' failed
The error most likely occurred in:

> ### Name: DCD
> ### Title: Differential Community Detection for Paired Biological Networks,
> ###   for e.g. case vs control
> ### Aliases: DCD
> 
> ### ** Examples
> 
> 
> DCD_output <- DCD()
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
..connectivity..
..matrix multiplication (system BLAS)..
..normalization..
..done.
> ## Not run: 
> ##D library(igraph)
> ##D g_A <- sample_grg(200, 0.15, torus=FALSE, coords = FALSE)
> ##D g_B <- permute(g_A,c(sample(20),21:200))
> ##D ground_truth <- c(rep(1,20),rep(0,180))
> ##D DCD_output2 <- DCD(g_A = g_A, g_B = g_B, method = "Spectral", mink = 7,
> ##D                    ground_truth = ground_truth, plot_flag = 1, color = "red",
> ##D                    iter = 1, cores = 1 )
> ##D   
> ## End(Not run)
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11146 (sockconn)
Execution halted
.makeICCDialog: no visible global function definition for 'J'
.makeICCDialog: no visible global function definition for 'new'
.makeICCDialog: no visible global function definition for '.jnull'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'new'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'J'
.makeNewFactorAnalysisDialog: no visible global function definition for
  'toJava'
.makeNewLDADialog: no visible global function definition for 'new'
.makeNewLDADialog: no visible global function definition for 'J'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'new'
.makeNewLDADialog : linkSubDialog: no visible global function
  definition for 'toJava'
.makeNewLDADialog: no visible global function definition for 'toJava'
.makeNewReliabilityDialog: no visible global function definition for
  'new'
.makeNewReliabilityDialog: no visible global function definition for
  'toJava'
.onLoad: no visible global function definition for '.jnull'
.onLoad: no visible global function definition for 'winMenuAdd'
.onLoad: no visible global function definition for 'winMenuAddItem'
.onLoad: no visible global function definition for 'jgr.getMenuNames'
.onLoad: no visible global function definition for 'jgr.insertMenu'
.onLoad: no visible global function definition for 'jgr.addMenu'
.onLoad: no visible global function definition for 'jgr.addMenuItem'
Undefined global functions or variables:
  .jnull J jgr.addMenu jgr.addMenuItem jgr.getMenuNames jgr.insertMenu
  new toJava winMenuAdd winMenuAddItem
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "winMenuAdd", "winMenuAddItem")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Running 'test-all.R' [27s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  -- 1. Failure: extract au (@test-pvclust_extract.R#12)  ------------------------
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  == testthat results  ===========================================================
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 10 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.2Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/diffMeanVar.Rcheck/00install.out' for details.
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11157 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11157 (sockconn)
Execution halted
Running examples in 'DiffNet-Ex.R' failed
The error most likely occurred in:

> ### Name: diffnet
> ### Title: Detection of Statistically Significant Changes in Paired
> ###   Biological Networks
> ### Aliases: diffnet
> 
> ### ** Examples
> 
> library("DiffNet")
> # this step is optional, it helps speed up calculations, run in parallel on 2 processors
> library(doParallel)
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> registerDoParallel(2)
> # Run the differential network analysis tehcnique on sample data
> p <- diffnet()
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11532 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11532 (sockconn)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'concepts.Rmd' using rmarkdown
--- finished re-building 'concepts.Rmd'

--- re-building 'convenience-features.Rmd' using rmarkdown
--- finished re-building 'convenience-features.Rmd'

--- re-building 'data-table-syntax.Rmd' using rmarkdown
--- finished re-building 'data-table-syntax.Rmd'

--- re-building 'glm.Rmd' using rmarkdown
--- finished re-building 'glm.Rmd'

--- re-building 'ingesting-data.Rmd' using rmarkdown
--- finished re-building 'ingesting-data.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\RtmpIbAxIE\file25bb0685132c7': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/DistributionOptimization.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   2.0Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
    libs   1.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/FastRWeb.Rcheck/00install.out' for details.
Running 'tinytest.R' [1s]
Running the tests in 'tests/tinytest.R' failed.
Complete output:
  > 
  > if ( requireNamespace("tinytest", quietly=TRUE) ){
  +   home <- length(unclass(packageVersion("fastshap"))[[1L]]) == 4
  +   tinytest::test_package("fastshap", at_home = home)
  + }
  Loading required package: Formula
  Loading required package: plotmo
  Loading required package: plotrix
  Loading required package: TeachingDemos
  
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    
  Running test_fastshap.R...............    0 tests    Error in fastshap:::genOMat(num_rows, num_cols) : 
    function 'enterRNGScope' not provided by package 'Rcpp'
  Calls: <Anonymous> ... run_test_dir -> lapply -> FUN -> eval -> eval -> <Anonymous>
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/fastStat.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/fdq.Rcheck/00install.out' for details.
Running 'testthat.R' [215s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [180s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  Registered S3 methods overwritten by 'forecast':
    method             from    
    fitted.fracdiff    fracdiff
    residuals.fracdiff fracdiff
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   5.1Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R   5.6Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.2Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/FuzzyR.Rcheck/00install.out' for details.
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   3.0Mb
    libs      1.4Mb
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    R         9.0Mb
    extdata   1.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R         2.4Mb
    extdata   2.2Mb
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.7Mb
plot.glmulti: no visible global function definition for 'windows'
glmulti,character-character-ANY-ANY: no visible global function
  definition for 'regsubsets'
Undefined global functions or variables:
  regsubsets windows
Consider adding
  importFrom("grDevices", "windows")
to your NAMESPACE file.
installed size is 30.9Mb
  sub-directories of 1Mb or more:
    R  30.9Mb
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11437 (sockconn)
Execution halted
Running examples in 'groupedSurv-Ex.R' failed
The error most likely occurred in:

> ### Name: groupedSurvFam
> ### Title: Compute the Efficient Score Statistic for the Frailty Model
> ### Aliases: groupedSurvFam
> 
> ### ** Examples
> 
> # Generate dummy data
> set.seed(111)
> n <- 24
> 
> # effect size
> beta <- 0.3
> 
> # covariate parameters
> theta <- c(0.2, 0.2)
> 
> # variable of interest
> MAF <- 0.05
> x <- matrix(rbinom(n, 2, MAF), ncol = 1)
> 
> # covariate data (centered at 0)
> z1 <- rnorm(n)
> z2 <- rbinom(n, 1, 0.5) - 0.5
> Z  <- matrix(cbind(z1, z2), ncol = 2)
> 
> # continuous survival time
> lam0 <- 1
> cmax <- 3
> lami <- lam0 * exp(x*beta + Z[,1]*theta[1]+Z[,2]*theta[2])
> stime <- rexp(n, lami)
> ctime <- runif(n, 0, cmax)
> delta <- stime < ctime
> otime <- pmin(stime, ctime)
> 
> # number of observation times
> ntps <- 5
> 
> # number of intervals
> r <- ntps + 1
> 
> # last observation time
> maxbreakq <- 0.85
> maxbreak <- qexp(maxbreakq, lam0)
> 
> # grouped failure times
> breaks <- (1:ntps) * (maxbreak/ntps)
> gtime <- findInterval(otime, breaks) + 1
> delta[gtime == r] <- FALSE
> dctime <- findInterval(ctime, breaks) + 1
> delta[gtime == dctime] <- FALSE
> delta <- as.numeric(delta)
> 
> # family-specific information
> m <- n/3
> fam_role <- rep(c("o","f","m"),m)
> fam_group <- as.character(rep(1:m,rep(3,m)))
> 
> # nuisance parameters
> alpha <- thetaEst(Z, gtime,delta)$alpha
> var <- 0.2
> 
> # compute efficient score statistics
> res   <- groupedSurvFam(x, fam_group, fam_role, alpha, var, gtime, delta) 
> res
            [,1]
[1,] -0.09108599
[2,] -0.03535880
[3,] -0.05805514
[4,] -0.07539618
[5,]  0.09537326
[6,]  0.50679716
[7,] -0.01163486
[8,] -0.02150784
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11733 (sockconn)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'ashg2012.Rnw' using Sweave
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-3.6.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.1/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'ashg2012.Rnw' failed with diagnostics:
running 'texi2dvi' on 'ashg2012.tex' failed

LaTeX errors:
! LaTeX Error: File `D:/RCompile/recent/R-36\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)

--- failed re-building 'ashg2012.Rnw'

SUMMARY: processing the following file failed:
  'ashg2012.Rnw'

Error: Vignette re-building failed.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/gwsem.Rcheck/00install.out' for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs   6.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      1.9Mb
installed size is 16.7Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.1Mb
    libs  13.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/ImpactEffectsize.Rcheck/00install.out' for details.
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 293
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11445 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11445 (sockconn)
Execution halted
Running examples in 'iRF-Ex.R' failed
The error most likely occurred in:

> ### Name: readForest
> ### Title: Pass data through a fitted forest, record node characteristics
> ###   [works for binary classification with continuous variables]
> ### Aliases: readForest
> 
> ### ** Examples
> 
>   n = 50; p = 10
>   X = array(rnorm(n*p), c(n, p))
>   Y = (X[,1]>0.35 & X[,2]>0.35)|(X[,5]>0.35 & X[,7]>0.35)
>   Y = as.factor(as.numeric(Y>0))
> 
>   train.id = 1:(n/2)
>   test.id = setdiff(1:n, train.id)
>   
>   rf <- randomForest(x=X, y=Y, keep.forest=TRUE, track.nodes=TRUE,
+     ntree=100)
>   rforest <- readForest(rfobj=rf, x=X, n.core=2)
>   head(rforest$tree_info)
NULL
> 
>  # count number of leaf nodes with at least 5 observations
>   sum(rforest$tree.info$size.node > 5)
[1] 284
> 
> 
> 
> 
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11255 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11255 (sockconn)
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs           4.3Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/JavaGD.Rcheck/00install.out' for details.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    java   6.0Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    doc    1.4Mb
    libs   2.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs       2.2Mb
    testdata   1.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
    proj   5.0Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   2.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/mdsOpt.Rcheck/00install.out' for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    libs  11.4Mb
Error(s) in re-building vignettes:
--- re-building 'A-quick-tour-of-NMoE.Rmd' using rmarkdown
--- finished re-building 'A-quick-tour-of-NMoE.Rmd'

--- re-building 'A-quick-tour-of-SNMoE.Rmd' using rmarkdown
--- finished re-building 'A-quick-tour-of-SNMoE.Rmd'

--- re-building 'A-quick-tour-of-StMoE.Rmd' using rmarkdown
Quitting from lines 103-105 (A-quick-tour-of-StMoE.Rmd) 
Error: processing vignette 'A-quick-tour-of-StMoE.Rmd' failed with diagnostics:
non-numeric argument to binary operator
--- failed re-building 'A-quick-tour-of-StMoE.Rmd'

--- re-building 'A-quick-tour-of-tMoE.Rmd' using rmarkdown
--- finished re-building 'A-quick-tour-of-tMoE.Rmd'

SUMMARY: processing the following file failed:
  'A-quick-tour-of-StMoE.Rmd'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: namespace 'flexmix' is not available and has been replaced
  Warning: namespace 'modeltools' is not available and has been replaced
  Warning: namespace 'kernlab' is not available and has been replaced
  Warning: namespace 'robustbase' is not available and has been replaced
See 'd:/Rcompile/CRANpkg/local/3.6/miRtest.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/mixKernel.Rcheck/00install.out' for details.
Package unavailable to check Rd xrefs: 'REBayes'
installed size is 23.7Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.0Mb
    libs  21.0Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
Found the following significant warnings:
  generateData.cpp:105:18: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 19; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/NestedCategBayesImpute.Rcheck/00install.out' for details.
installed size is 18.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.7Mb
    R         5.8Mb
    include   5.6Mb
    libs      1.8Mb
    tests     1.5Mb
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  -- 1. Error: (unknown) (@test_randomcluster.R#4)  ------------------------------
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [36s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(NLMR)
  > 
  > test_check("NLMR")
  Failed with error:  'there is no package called 'igraph''
  -- 1. Error: (unknown) (@test_randomcluster.R#4)  ------------------------------
  you need to install the igraph package to be able to use this function
  Backtrace:
   1. base::suppressWarnings(...)
   3. NLMR::nlm_randomcluster(...)
   5. raster::clump(ranclumap, direction = neighbourhood, gaps = FALSE)
   6. raster:::.local(x, ...)
  
  == testthat results  ===========================================================
  [ OK: 63 | SKIPPED: 0 | WARNINGS: 3 | FAILED: 1 ]
  1. Error: (unknown) (@test_randomcluster.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'NUCOMBog.ltx' using tex
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "NUCOMBog.ltx" --max-iterations=20 -I "D:/RCompile/recent/R-3.6.1/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.6.1/share/texmf/bibtex/bst"' had status 1
Error: processing vignette 'NUCOMBog.ltx' failed with diagnostics:
Failed to locate the 'weave' output file (by engine 'R.rsp::tex') for vignette with name 'NUCOMBog'. The following files exist in directory '.': 'NUCOMBog.ltx', 'library.bib'
--- failed re-building 'NUCOMBog.ltx'

SUMMARY: processing the following file failed:
  'NUCOMBog.ltx'

Error: Vignette re-building failed.
Execution halted
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.5Mb
    libs   2.0Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   1.9Mb
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    R        2.5Mb
    libs     7.2Mb
    models   4.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/pbdBASE.Rcheck/00install.out' for details.
Running examples in 'penDvine-Ex.R' failed
The error most likely occurred in:

> ### Name: penDvine-package
> ### Title: The package 'penDvine' offers routines for estimating densities
> ###   and copula distribution of D-vines.
> ### Aliases: penDvine-package
> 
> ### ** Examples
> 
> #This examples describes the estimation of a D-vine to winddata,
> #available in this package. After the margins are prepared, we estimate a
> #D-vine using B-splines with 9 (K+1) marginal knots and penalizing second (m=2)
> #order differences (pen=1) of the basis coefficients.
> 
> data(Winddata)
> ex.data<-Winddata[c(1:100),c(1:4)] #examplary subdata for fast calculation
> wind.example<-Dvine(ex.data,K=7,pen=1,lambda=100,order.Dvine=FALSE,base="B-spline",m=2,cores=2)
>   
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11974 (sockconn)
	<-CRANwin.fb05.statistik.uni-dortmund.de:11974 (sockconn)
Execution halted
Error(s) in re-building vignettes:
--- re-building 'artificial_intelligence_evolution.Rmd' using rmarkdown
--- finished re-building 'artificial_intelligence_evolution.Rmd'

--- re-building 'gas_influx_overbalanced.Rmd' using rmarkdown
Quitting from lines 44-61 (gas_influx_overbalanced.Rmd) 
Error: processing vignette 'gas_influx_overbalanced.Rmd' failed with diagnostics:
HTTP error 500.
--- failed re-building 'gas_influx_overbalanced.Rmd'

--- re-building 'gas_lift_keywords_variation.Rmd' using rmarkdown
--- finished re-building 'gas_lift_keywords_variation.Rmd'

SUMMARY: processing the following file failed:
  'gas_influx_overbalanced.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   1.7Mb
Running 'testthat.R' [79s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(phenocamapi)
  Loading required package: data.table
  Loading required package: rjson
  Loading required package: RCurl
  Loading required package: bitops
  > library(data.table)
  > 
  > test_check("phenocamapi")
  trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
  Content type 'application/octet-stream' length 194443 bytes (189 KB)
  ==================================================
  downloaded 189 KB
  
  Error in file(con, "r") : cannot open the connection
  -- 1. Error: (unknown) (@testphenocamapi.R#18)  --------------------------------
  a character vector argument expected
  Backtrace:
   1. base::basename(duke_middays[1])
  
  == testthat results  ===========================================================
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 1 ]
  1. Error: (unknown) (@testphenocamapi.R#18) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'getting_started_phenocam_api.Rmd' using rmarkdown
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 194443 bytes (189 KB)
==================================================
downloaded 189 KB

Quitting from lines 258-272 (getting_started_phenocam_api.Rmd) 
Error: processing vignette 'getting_started_phenocam_api.Rmd' failed with diagnostics:
'url' must be a length-one character vector
--- failed re-building 'getting_started_phenocam_api.Rmd'

--- re-building 'phenocam_data_fusion.Rmd' using rmarkdown
Loading required package: rjson
Loading required package: RCurl
Loading required package: bitops
trying URL 'http://phenocam.sr.unh.edu/data/archive/dukehw/ROI/dukehw_DB_1000_3day.csv'
Content type 'application/octet-stream' length 194443 bytes (189 KB)
==================================================
downloaded 189 KB

trying URL 'http://phenocam.sr.unh.edu/data/archive/oregonMP/ROI/oregonMP_EN_1000_3day.csv'
Content type 'application/octet-stream' length 261492 bytes (255 KB)
==================================================
downloaded 255 KB

--- finished re-building 'phenocam_data_fusion.Rmd'

SUMMARY: processing the following file failed:
  'getting_started_phenocam_api.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      6.9Mb
    data   2.5Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    java   5.1Mb
Found the following significant warnings:
  StandardizeString.cpp:13:25: warning: passing NULL to non-pointer argument 1 of 'Rcpp::Vector<RTYPE, StoragePolicy>::Vector(const int&) [with int RTYPE = 16; StoragePolicy = Rcpp::PreserveStorage]' [-Wconversion-null]
See 'd:/Rcompile/CRANpkg/local/3.6/PPRL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/prettydoc.Rcheck/00install.out' for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    R         1.7Mb
    contrib   3.6Mb
    doc       2.9Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs   3.1Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/randstr.Rcheck/00install.out' for details.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/Rblpapi.Rcheck/00install.out' for details.
installed size is 23.3Mb
  sub-directories of 1Mb or more:
    cont  23.3Mb
Running 'testthat_p1.R' [13s]
  Running 'testthat_p2.R' [3s]
  Running 'testthat_p3.R' [16s]
  Running 'testthat_p4.R' [2s]
  Running 'testthat_p5.R' [17s]
Running the tests in 'tests/testthat_p3.R' failed.
Complete output:
  > #testing Randy Zwitch solution
  > 
  > library(testthat)
  > library(RClone)
  > test_check("RClone", filter = "p3")
  [1] "Number of MLG sim = 9"
  -- 1. Failure: the genet_dist functions work (@test_package_RClone_p3.R#19)  ---
  length(prev2[[1]]) not equal to 45.
  1/1 mismatches
  [1] 36 - 45 == -9
  
  == testthat results  ===========================================================
  [ OK: 46 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: the genet_dist functions work (@test_package_RClone_p3.R#19) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RcmdrPlugin.BiclustGUI.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    include   7.7Mb
    libs      1.8Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    include   1.8Mb
    lib       8.9Mb
    libs      1.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/RCurl.Rcheck/00install.out' for details.
Found the following significant warnings:
  skein_block64.c:226:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.6/RDieHarder.Rcheck/00install.out' for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    java  10.1Mb
Running 'testthat.R' [58s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(recipes)
  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
  
  
  Attaching package: 'recipes'
  
  The following object is masked from 'package:stats':
  
      step
  
  > 
  > test_check(package = "recipes")
  1 package is needed for this model and is not installed. (NMF). Start a clean R session then run: install.packages("NMF")-- 1. Error: quasiquotation (@test_slice.R#40)  --------------------------------
  `call` must be a call
  
  == testthat results  ===========================================================
  [ OK: 1394 | SKIPPED: 7 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: quasiquotation (@test_slice.R#40) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   2.3Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    java   5.2Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/Rglpk.Rcheck/00install.out' for details.
installed size is 20.8Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  10.7Mb
    libs   5.1Mb
File 'RGtk2/libs/i386/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'
File 'RGtk2/libs/x64/RGtk2.dll':
  Found non-API calls to R: 'R_new_custom_connection',
    'Rf_EncodeInteger', 'Rf_EncodeLogical', 'Rf_EncodeReal',
    'Rf_formatInteger', 'Rf_formatLogical', 'Rf_formatReal'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/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/3.6/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.6/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 10.8Mb
  sub-directories of 1Mb or more:
    java  10.8Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    extdata   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rlang.Rcheck/00install.out' for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    java  12.1Mb
Running examples in 'robustHD-Ex.R' failed
The error most likely occurred in:

> ### Name: AIC.seqModel
> ### Title: Information criteria for a sequence of regression models
> ### Aliases: AIC.seqModel AIC.sparseLTS BIC.seqModel BIC.sparseLTS
> ### Keywords: regression
> 
> ### ** Examples
> 
> ## generate data
> # example is not high-dimensional to keep computation time low
> library("mvtnorm")
> set.seed(1234)  # for reproducibility
> n <- 100  # number of observations
> p <- 25   # number of variables
> beta <- rep.int(c(1, 0), c(5, p-5))  # coefficients
> sigma <- 0.5      # controls signal-to-noise ratio
> epsilon <- 0.1    # contamination level
> Sigma <- 0.5^t(sapply(1:p, function(i, j) abs(i-j), 1:p))
> x <- rmvnorm(n, sigma=Sigma)    # predictor matrix
> e <- rnorm(n)                   # error terms
> i <- 1:ceiling(epsilon*n)       # observations to be contaminated
> e[i] <- e[i] + 5                # vertical outliers
> y <- c(x %*% beta + sigma * e)  # response
> x[i,] <- x[i,] + 5              # bad leverage points
> 
> 
> ## robust LARS
> # fit model
> fitRlars <- rlars(x, y, sMax = 10)
Error in rlars.default(x, y, sMax = 10) : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: rlars -> rlars.default
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    1.8Mb
    tests   1.2Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
Running examples in 'rrcovHD-Ex.R' failed
The error most likely occurred in:

> ### Name: SosDiscRobust
> ### Title: Robust and sparse multigroup classification by the optimal
> ###   scoring approach
> ### Aliases: SosDiscRobust SosDiscRobust.default SosDiscRobust.formula
> ### Keywords: robust multivariate classification sparse
> 
> ### ** Examples
> 
> 
> ## EXAMPLE 1 ######################################
> data(olitos)
> grind <- which(colnames(olitos)=="grp")
> 
> set.seed(5008642)
> mod <- SosDiscRobust(grp~., data=olitos, lambda=0.3, maxIte=30, Q=3, tol=1e-2)
Error in callBackend("R_sparseSubsets", R_x = x, R_y = y, R_lambda = lambda,  : 
  function 'dataptr' not provided by package 'Rcpp'
Calls: SosDiscRobust ... sparseLTS.default -> fastSparseLTS -> sparseSubsets -> callBackend
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/RSDA.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/3.6/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/3.6/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/3.6/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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/rstap.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   3.2Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    Lib  11.5Mb
Math.Sym: no visible binding for global variable 'transtab'
jythonStart: no visible global function definition for '.jinit'
jythonStart: no visible global function definition for '.jnew'
jythonStart: no visible binding for global variable '.Jython'
sympy: no visible binding for global variable '.Jython'
sympy: no visible global function definition for '.jstrVal'
sympyStart: no visible binding for global variable '.Jython'
Undefined global functions or variables:
  .Jython .jinit .jnew .jstrVal transtab
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.8Mb
    projects   2.7Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   1.8Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    include   3.9Mb
    libs      8.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/SanzCircos.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    R   7.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   2.9Mb
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   4.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   2.6Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.2Mb
    libs   1.2Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > test_check("SqlRender")
  Loading required package: SqlRender
  Reading SQL from package folder: D:/temp/Rtmpm4AYl2/RLIBS_a56441ac289b/SqlRender/sql/sql_server/test.sql
  Writing R function to: D:\temp\RtmpkDo4zP\filee6f85f385711
  -- 1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(render("{true = true} ? {true} : {false}"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  -- 2. Error: translate sql server throws error when invalid target is given (@te
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(translate("iSELECT * FROM a;", targetDialect = "pwd"))
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  -- 3. Error: translateSingleStatement sql server -> oracle throw error if > 1 st
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  == testthat results  ===========================================================
  [ OK: 448 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: If-then-else: error on bad boolean logic syntax (@test-renderSql.R#155) 
  2. Error: translate sql server throws error when invalid target is given (@test-translateSql.R#394) 
  3. Error: translateSingleStatement sql server -> oracle throw error if > 1 statement (@test-translateSql.R#2338) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    doc    3.0Mb
    libs   1.6Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/STraTUS.Rcheck/00install.out' for details.
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/symbolicDA.Rcheck/00install.out' for details.
Running 'testthat.R' [44s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library("testthat")
  > library("tabulizer")
  > 
  > stop_logging()
  > test_check("tabulizer")
  -- 1. Error: Extract from encrypted PDF (@test_extract_tables.R#64)  -----------
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(extract_tables(f6, password = "wrongpassword"))
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  == testthat results  ===========================================================
  [ OK: 86 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: Extract from encrypted PDF (@test_extract_tables.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'tealeaves-intermediate.Rmd' using rmarkdown
--- finished re-building 'tealeaves-intermediate.Rmd'

Warning in file(con, "r") :
  cannot open file 'D:\temp\Rtmp6jiL0t\file217c02d382e8a': Permission denied
Error in file(con, "r") : cannot open the connection
Calls: <Anonymous> -> readLines -> file
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
   0.02    0.00    2.08 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11910 (sockconn)
Execution halted
Running examples in 'text2vec-Ex.R' failed
The error most likely occurred in:

> ### Name: itoken
> ### Title: Iterators (and parallel iterators) over input objects
> ### Aliases: itoken itoken.list itoken.character itoken.iterator
> ###   itoken_parallel itoken_parallel.character
> ###   itoken_parallel.ifiles_parallel itoken_parallel.list
> 
> ### ** Examples
> 
> data("movie_review")
> txt = movie_review$review[1:100]
> ids = movie_review$id[1:100]
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10)
> it = itoken(txt, tolower, word_tokenizer, n_chunks = 10, ids = ids)
> # Example of stemming tokenizer
> # stem_tokenizer =function(x) {
> #   lapply(word_tokenizer(x), SnowballC::wordStem, language="en")
> # }
> #------------------------------------------------
> # PARALLEL iterators
> #------------------------------------------------
> library(text2vec)
> 
> N_WORKERS = 1 # change 1 to number of cores in parallel backend
> if(require(doParallel)) registerDoParallel(N_WORKERS)
Loading required package: doParallel
Loading required package: foreach
Loading required package: iterators
Loading required package: parallel
> data("movie_review")
> it = itoken_parallel(movie_review$review[1:100], n_chunks = N_WORKERS)
> system.time(dtm <- create_dtm(it, hash_vectorizer(2**16), type = 'dgTMatrix'))
   user  system elapsed 
    0.0     0.0     2.9 
> 
> 
> 
> cleanEx()

detaching 'package:doParallel', 'package:parallel',
  'package:iterators', 'package:foreach'

Error: connections left open:
	<-CRANwin.fb05.statistik.uni-dortmund.de:11956 (sockconn)
Execution halted
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/tth.Rcheck/00install.out' for details.
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    doc     6.3Mb
    ubinc   1.9Mb
Running examples in 'UniprotR-Ex.R' failed
The error most likely occurred in:

> ### Name: ConvertID
> ### Title: Connect and parse UniProt database identifiers information.
> ### Aliases: ConvertID
> 
> ### ** Examples
> 
> Obj <- ConvertID("O14520" , "ACC+ID" , "EMBL")
Warning in file(file, "rt") :
  cannot open URL 'https://www.uniprot.org/uploadlists/?query=O14520&format=tab&from=ACC+ID&to=EMBL': HTTP status was '504 Gateway Timeout'
Error in file(file, "rt") : cannot open the connection
Calls: ConvertID -> read.table -> file
Execution halted
Error(s) in re-building vignettes:
--- re-building 'vdmR-vignette.Rnw' using knitr
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
Quitting from lines 189-193 (vdmR-vignette.Rnw) 
Error: processing vignette 'vdmR-vignette.Rnw' failed with diagnostics:
missing value where TRUE/FALSE needed
--- failed re-building 'vdmR-vignette.Rnw'

SUMMARY: processing the following file failed:
  'vdmR-vignette.Rnw'

Error: Vignette re-building failed.
Execution halted
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    R      3.9Mb
    doc    1.2Mb
    help   2.9Mb
Running 'testthat.R' [221s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(weathercan)
  > 
  > Sys.setenv("R_TESTS" = "")
  > 
  > test_check("weathercan")
  -- 1. Error: normals_raw() download normals as character  ----------------------
  cannot open the connection
  Backtrace:
    1. testthat::expect_silent(normals_raw(url))
    9. weathercan:::normals_raw(url)
   10. base::readLines(con <- url(loc, encoding = "latin1"), n = nrows)
  
  -- 2. Error: normals_extract() / frost_extract() extract data (@test_08_normals.
  cannot open the connection
  Backtrace:
    1. base::paste0(...)
    9. weathercan:::normals_raw(.)
   10. base::readLines(con <- url(loc, encoding = "latin1"), n = nrows)
  
  -- 3. Error: normals_format()/frost_format() format data to correct class (@test
  cannot open the connection
  Backtrace:
    1. base::paste0(...)
    9. weathercan:::normals_raw(.)
   10. base::readLines(con <- url(loc, encoding = "latin1"), n = nrows)
  
  -- 4. Error: normals_dl() downloads normals/frost dates as tibble  -------------
  The link in `options("weathecan.urls.normals")` must point to the site where climate normals are stored by province
  Backtrace:
   1. testthat::expect_silent(normals_dl(climate_id = "5010480"))
   9. weathercan::normals_dl(climate_id = "5010480")
  
  == testthat results  ===========================================================
  [ OK: 544 | SKIPPED: 5 | WARNINGS: 2 | FAILED: 4 ]
  1. Error: normals_raw() download normals as character 
  2. Error: normals_extract() / frost_extract() extract data (@test_08_normals.R#26) 
  3. Error: normals_format()/frost_format() format data to correct class (@test_08_normals.R#36) 
  4. Error: normals_dl() downloads normals/frost dates as tibble 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building 'flags.Rmd' using rmarkdown

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 66-69 (flags.Rmd) 
Error: processing vignette 'flags.Rmd' failed with diagnostics:
The link in `options("weathecan.urls.normals")` must point to the site where climate normals are stored by province
--- failed re-building 'flags.Rmd'

--- re-building 'glossary.Rmd' using rmarkdown
--- finished re-building 'glossary.Rmd'

--- re-building 'glossary_normals.Rmd' using rmarkdown
--- finished re-building 'glossary_normals.Rmd'

--- re-building 'interpolate_data.Rmd' using rmarkdown

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

--- finished re-building 'interpolate_data.Rmd'

--- re-building 'normals.Rmd' using rmarkdown

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 39-41 (normals.Rmd) 
Error: processing vignette 'normals.Rmd' failed with diagnostics:
The link in `options("weathecan.urls.normals")` must point to the site where climate normals are stored by province
--- failed re-building 'normals.Rmd'

--- re-building 'weathercan.Rmd' using rmarkdown

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

--- finished re-building 'weathercan.Rmd'

SUMMARY: processing the following files failed:
  'flags.Rmd' 'normals.Rmd'

Error: Vignette re-building failed.
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    bn   7.1Mb
Found the following notes/warnings:
  Non-staged installation was used
See 'd:/Rcompile/CRANpkg/local/3.6/x13binary.Rcheck/00install.out' for details.
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    java   9.8Mb
Error(s) in re-building vignettes:
--- re-building ‘aaSEA_Documentation.Rmd’ using rmarkdown
Warning 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 RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in RColorBrewer::brewer.pal(N, "Set2") :
  n too large, allowed maximum for palette Set2 is 8
Returning the palette you asked for with that many colors

Warning in normalizePath(f2) :
  path[1]="webshot3f472895632b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot3f472895632b.png': No such file or directory
Quitting from lines 90-91 (aaSEA_Documentation.Rmd) 
Error: processing vignette 'aaSEA_Documentation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘aaSEA_Documentation.Rmd’

SUMMARY: processing the following file failed:
  ‘aaSEA_Documentation.Rmd’

Error: Vignette re-building 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/3.6/abcdeFBA.Rcheck/00install.out’ for details.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   2.6Mb
    libs   2.3Mb
Namespaces in Imports field not imported from:
  ‘httr’ ‘progress’
  All declared Imports should be used.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is 13.7Mb
  sub-directories of 1Mb or more:
    R  13.7Mb
Package required but not available: ‘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/3.6/adamethods.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘adapt_demo.Rmd’ using rmarkdown
Warning 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 'adapt_demo.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adapt_demo.Rmd’

SUMMARY: processing the following file failed:
  ‘adapt_demo.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages required but not available: 'WGCNA', 'DeconRNASeq'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    data       2.8Mb
    pictures   2.1Mb
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/3.6/ade4TkGUI.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘amigaDiskFiles.Rmd’ using rmarkdown
Warning 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 'amigaDiskFiles.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘amigaDiskFiles.Rmd’

SUMMARY: processing the following file failed:
  ‘amigaDiskFiles.Rmd’

Error: Vignette re-building 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/3.6/adiv.Rcheck/00install.out’ for details.
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Packages suggested but not available for checking:
  'rioja', 'HiTC', 'snpStats', 'BiocGenerics'
Packages unavailable to check Rd xrefs: ‘HiTC’, ‘snpStats’
Error(s) in re-building vignettes:
  ...
--- re-building ‘adpss_ex.Rmd’ using rmarkdown
Warning 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 'adpss_ex.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘adpss_ex.Rmd’

SUMMARY: processing the following file failed:
  ‘adpss_ex.Rmd’

Error: Vignette re-building 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/3.6/afCEC.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘afpt-aerodynamic-model.Rmd’ using rmarkdown
Warning 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 'afpt-aerodynamic-model.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-aerodynamic-model.Rmd’

--- re-building ‘afpt-basic-usage.Rmd’ using rmarkdown
Warning 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 'afpt-basic-usage.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-basic-usage.Rmd’

--- re-building ‘afpt-multiple-birds.Rmd’ using rmarkdown
Warning 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 'afpt-multiple-birds.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘afpt-multiple-birds.Rmd’

SUMMARY: processing the following files failed:
  ‘afpt-aerodynamic-model.Rmd’ ‘afpt-basic-usage.Rmd’
  ‘afpt-multiple-birds.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘agridat-Ex.R’ failed
The error most likely occurred in:

> ### Name: baker.wheat.uniformity
> ### Title: Uniformity trial of wheat
> ### Aliases: baker.wheat.uniformity
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(baker.wheat.uniformity)
> dat <- baker.wheat.uniformity
> 
> require(desplot)
Loading required package: desplot
Error: package or namespace load failed for ‘desplot’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘stringi’
> desplot(yield ~ col*row, dat,
+         flip=TRUE, aspect=1,
+         main="baker.wheat.uniformity")
Error in desplot(yield ~ col * row, dat, flip = TRUE, aspect = 1, main = "baker.wheat.uniformity") : 
  could not find function "desplot"
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘agridat_data.Rmd’ using rmarkdown
Warning 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 'agridat_data.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_data.Rmd’

--- re-building ‘agridat_examples.Rmd’ using rmarkdown
Warning 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 'agridat_examples.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_examples.Rmd’

--- re-building ‘agridat_papadakis.Rmd’ using rmarkdown
Warning 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 'agridat_papadakis.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘agridat_papadakis.Rmd’

SUMMARY: processing the following files failed:
  ‘agridat_data.Rmd’ ‘agridat_examples.Rmd’ ‘agridat_papadakis.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘ahn.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘ahn.Rmd’

SUMMARY: processing the following file failed:
  ‘ahn.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Biostrings’
Packages unavailable to check Rd xrefs: ‘Biostrings’, ‘Starr’
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/3.6/AIG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ggseas’
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/3.6/akmedoids.Rcheck/00install.out’ for details.
Package required but not available: ‘org.Hs.eg.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
File ‘allelic/libs/allelic.so’:
  Found ‘___stderrp’, possibly from ‘stderr’ (C)
    Object: ‘newallelic.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
Found the following significant warnings:
  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/3.6/alphashape3d.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.6Mb
Package suggested but not available for checking: ‘Biobase’
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    extdata  11.4Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.6Mb
Errors in running code in vignettes:
when running code in ‘amelia.Rnw’
  ...
Loading required package: Zelig
Loading required package: survival
Error: package or namespace load failed for ‘Zelig’ in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called ‘openxlsx’

> z5 <- zls$new()

  When sourcing ‘amelia.R’:
Error: object 'zls' not found
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘amen.Rnw’ using knitr
Loading required package: network
network: Classes for Relational Data
Version 1.15 created on 2019-04-01.
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 24.0Mb
  sub-directories of 1Mb or more:
    libs  22.6Mb
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/3.6/analogueExtra.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/3.6/AnalyzeFMRI.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/3.6/animalTrack.Rcheck/00install.out’ for details.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    cereal   1.4Mb
    libs    25.4Mb
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    libs   2.1Mb
Package suggested but not available for checking: ‘rhdf5’
Running ‘testthat.R’ [80s/128s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 381 SKIPPED: 0 FAILED: 25
  1. Error: h5 : processing correctBalance when mcYear is set to NULL (@test-correctBalance.R#72) 
  2. Error: h5 : processing correctBalance when mcYear is set to 1 (@test-correctBalance.R#108) 
  3. Error: h5 : processing correctBalance when mcYear is set to 1 for weekly or monthly data (@test-correctBalance.R#146) 
  4. Error: h5 : processing correctBalance when mcYear is set to 1 for monthly data on districts (@test-correctBalance.R#227) 
  5. Error: h5 : processing correctBalance with addProcessingH5 (@test-correctBalance.R#273) 
  6. Error: h5 : processing, write results (@test-h5_processing.R#4) 
  7. Error: h5 : processing, write results mcAll (@test-h5_processing.R#30) 
  8. Error: h5 : all data (@test-h5_processing.R#56) 
  9. Error: h5 : processing calc by user (@test-h5_processing.R#72) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘antares.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘antares.Rmd’

--- re-building ‘antaresH5.Rmd’ using rmarkdown
Warning 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 38-72 (antaresH5.Rmd) 
Error: processing vignette 'antaresH5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘antaresH5.Rmd’

SUMMARY: processing the following file failed:
  ‘antaresH5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 105.7Mb
  sub-directories of 1Mb or more:
    libs  105.2Mb
Packages suggested but not available for checking: 'Biostrings', 'kebabs'
Error(s) in re-building vignettes:
--- re-building ‘labs.Rmd’ using rmarkdown
Warning 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 32-34 (labs.Rmd) 
Error: processing vignette 'labs.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘labs.Rmd’

--- re-building ‘lines.Rmd’ using rmarkdown
Warning 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 39-40 (lines.Rmd) 
Error: processing vignette 'lines.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘lines.Rmd’

--- re-building ‘starting-with-apexcharts.Rmd’ using rmarkdown
Warning 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 36-40 (starting-with-apexcharts.Rmd) 
Error: processing vignette 'starting-with-apexcharts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘starting-with-apexcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘labs.Rmd’ ‘lines.Rmd’ ‘starting-with-apexcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
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/3.6/aqr.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/3.6/archiDART.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘argparse.Rrst’ using knitr
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
--- failed re-building ‘argparse.Rrst’

SUMMARY: processing the following file failed:
  ‘argparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘AffymetrixDataTestFiles’
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R             2.3Mb
    help          1.2Mb
    testScripts   1.1Mb
Package suggested but not available for checking: ‘affxparser’
Package unavailable to check Rd xrefs: ‘affxparser’
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/3.6/Arothron.Rcheck/00install.out’ for details.
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    libs  22.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    extdata   3.7Mb
    libs      1.3Mb
Packages suggested but not available for checking: 'graph', 'Rgraphviz'
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
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/3.6/audio.Rcheck/00install.out’ for details.
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  14.9Mb
Packages required but not available:
  'org.Hs.eg.db', 'ConsensusClusterPlus', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  24.8Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/babel.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BACA.Rcheck/00install.out’ for details.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   2.7Mb
Package suggested but not available for checking: ‘pcalg’
Package unavailable to check Rd xrefs: ‘pcalg’
installed size is 61.8Mb
  sub-directories of 1Mb or more:
    libs  60.9Mb
Running ‘test-all.R’ [1s/2s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Need at least two classes to do classification.
  1: samme(activity ~ ., train, test, 3, ntree = 5, trace = F) at /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bagRboostR.Rcheck/bagRboostR/tests/test_samme.R:6
  2: randomForest(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  3: randomForest.formula(formula, data = t, do.trace = trace, ntree = ntree, mtry = mtry)
  4: randomForest.default(m, y, ...)
  5: stop("Need at least two classes to do classification.")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 39 SKIPPED: 0 FAILED: 1
  1. Error: samme returns a character vector of predicted classes (@test_samme.R#6) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  Placing tests in `inst/tests` is deprecated. Please use `tests/testthat` instead 
  Execution halted
Package suggested but not available for checking: ‘philr’
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/3.6/BALCONY.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘base’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BALLI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bapred.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.1Mb
    libs   3.4Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   3.0Mb
installed size is 13.5Mb
  sub-directories of 1Mb or more:
    libs  13.4Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/baseflow.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘article2-vignette.Rnw’ using knitr

Execution halted
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/3.6/BAT.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/3.6/BAwiR.Rcheck/00install.out’ for details.
installed size is 52.3Mb
  sub-directories of 1Mb or more:
    libs  51.3Mb
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/3.6/bayesCL.Rcheck/00install.out’ for details.
installed size is 54.1Mb
  sub-directories of 1Mb or more:
    libs  53.3Mb
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    doc    5.4Mb
    libs  12.9Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   4.0Mb
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  17.8Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    ex-data   4.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BayesXsrc.Rcheck/00install.out’ for details.
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  5.9Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      3.1Mb
Error(s) in re-building vignettes:
--- re-building ‘article.Rnw’ using Sweave
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Setting levels: control = No, case = Yes
Loading required package: Biostrings
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: S4Vectors
Warning: package 'S4Vectors' was built under R version 3.6.1
Loading required package: stats4

Attaching package: 'S4Vectors'

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

    expand.grid

Loading required package: IRanges
Warning: package 'IRanges' was built under R version 3.6.1
Loading required package: XVector

Attaching package: 'Biostrings'

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

    strsplit

Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'article.Rnw'

SUMMARY: processing the following file failed:
  'article.Rnw'

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  sparseFactor.cpp:33:10: warning: explicitly assigning value of variable of type 'Rcpp::IntegerVector' (aka 'Vector<13>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BClustLonG.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘DNAcopy’
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/3.6/bcROCsurface.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'beadarrayExampleData', 'lumi'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/beadarrayFilter.Rcheck/00install.out’ for details.
Package required but not available: ‘rggobi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 69.3Mb
  sub-directories of 1Mb or more:
    libs  67.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘beanz_vignettes.Rmd’ using rmarkdown
Warning 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
Error(s) in re-building vignettes:
  ...
--- re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-74 (abcd-laagdrempelige_nederlandse_uitleg.Rmd) 
Error: processing vignette 'abcd-laagdrempelige_nederlandse_uitleg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

--- re-building ‘abcd.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘abcd.Rmd’

--- re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘matrix-van-aspecten-van-de-psychologie.Rmd’

SUMMARY: processing the following file failed:
  ‘abcd-laagdrempelige_nederlandse_uitleg.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 36.1Mb
  sub-directories of 1Mb or more:
    libs  35.1Mb
installed size is 149.6Mb
  sub-directories of 1Mb or more:
    include  149.6Mb
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.4Mb
Package required but not available: ‘Rmpi’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
Error(s) in re-building vignettes:
--- re-building ‘analysis.Rmd’ using rmarkdown
Warning 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]="webshotec59687b63.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotec59687b63.png': No such file or directory
Quitting from lines 245-248 (analysis.Rmd) 
Error: processing vignette 'analysis.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘analysis.Rmd’

--- re-building ‘methodology.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘methodology.Rmd’

SUMMARY: processing the following file failed:
  ‘analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rmpi’
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    doc       3.0Mb
    extdata   2.5Mb
    libs      2.0Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    extdata   2.3Mb
    libs      7.5Mb
installed size is 17.5Mb
  sub-directories of 1Mb or more:
    libs  17.0Mb
Error(s) in re-building vignettes:
--- re-building ‘billboarder-intro.Rmd’ using rmarkdown
Warning 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 41-48 (billboarder-intro.Rmd) 
Error: processing vignette 'billboarder-intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘billboarder-intro.Rmd’

--- re-building ‘billboarder-mapping.Rmd’ using rmarkdown
Warning 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 44-46 (billboarder-mapping.Rmd) 
Error: processing vignette 'billboarder-mapping.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘billboarder-mapping.Rmd’

--- re-building ‘billboarder-options.Rmd’ using rmarkdown
Warning 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 26-29 (billboarder-options.Rmd) 
Error: processing vignette 'billboarder-options.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘billboarder-options.Rmd’

--- re-building ‘billboarder.Rmd’ using rmarkdown
Warning 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 37-56 (billboarder.Rmd) 
Error: processing vignette 'billboarder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘billboarder.Rmd’

SUMMARY: processing the following files failed:
  ‘billboarder-intro.Rmd’ ‘billboarder-mapping.Rmd’
  ‘billboarder-options.Rmd’ ‘billboarder.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   2.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bioacoustics.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘BioCircos.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘BioCircos.Rmd’

SUMMARY: processing the following file failed:
  ‘BioCircos.Rmd’

Error: Vignette re-building failed.
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/3.6/Biocomb.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/3.6/BiodiversityR.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    doc       2.5Mb
    extdata   8.1Mb
Packages required but not available: 'ChemmineR', 'fmcsR', 'org.Hs.eg.db'

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/3.6/bios2mds.Rcheck/00install.out’ for details.
Package required but not available: ‘rpanel’

Package suggested but not available for checking: ‘soilphysics’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package listed in more than one of Depends, Imports, Suggests, Enhances:
  ‘colorspace’
A package should be listed in only one of these fields.
Packages in Depends field not imported from:
  ‘deldir’ ‘rgl’ ‘tcltk’ ‘tcltk2’ ‘tkrplot’
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Packages suggested but not available for checking: 'GO.db', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/BiSEp.Rcheck/00install.out’ for details.
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [5s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(blastula)
  > 
  > test_check("blastula")
  ── 1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10)  ───────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(rmd_path, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 188 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: knitr_sidecar_prefix preconditions hold (@test-utils.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 51.4Mb
  sub-directories of 1Mb or more:
    libs  49.7Mb
installed size is 34.8Mb
  sub-directories of 1Mb or more:
    libs  33.5Mb
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 36.8Mb
  sub-directories of 1Mb or more:
    libs  36.5Mb
Packages suggested but not available for checking:
  'graph', 'gRain', 'gRbase', 'Rgraphviz'
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package unavailable to check Rd xrefs: ‘gRain’
Error(s) in re-building vignettes:
  ...
--- re-building ‘methods.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘methods.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

--- re-building ‘usage.rmd’ using rmarkdown
Warning 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 121-122 (usage.rmd) 
Error: processing vignette 'usage.rmd' failed with diagnostics:
Package graph needed 
--- failed re-building ‘usage.rmd’

SUMMARY: processing the following file failed:
  ‘usage.rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'graph', 'Rgraphviz', 'gRain'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.1Mb
Package suggested but not available for checking: ‘sangerseqR’
installed size is 335.2Mb
  sub-directories of 1Mb or more:
    include    8.5Mb
    lib      326.4Mb
installed size is 75.9Mb
  sub-directories of 1Mb or more:
    libs  75.4Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/bootsPLS.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘qvalue’
Package unavailable to check Rd xrefs: ‘qvalue’
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/3.6/bpca.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
No protocol specified

(R:60058): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
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/3.6/brainKCCA.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/3.6/brainR.Rcheck/00install.out’ for details.
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 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
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$data)
> # Use more than 80 iterations and 4 chains for serious fits
> fit = stan_fit(data, chains = 1, iter = 80)
error occurred during calling the sampler; sampling not done
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Stan model 'breath_test_1' does not contain samples.
Error in data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2),  : 
  arguments imply differing number of rows: 120, 0
Calls: stan_fit -> data.frame
Execution halted
Running ‘testthat.R’ [6s/13s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  arguments imply differing number of rows: 500, 0
  1: stan_fit(data, dose = dose, student_t_df = student_t_df, chains = chains, iter = iter) at testthat/test_stan_fit_2.R:21
  2: data.frame(pat_group_i = rep(1:n_record, each = chains * iter/2), m = as.vector(rstan::extract(fit, 
         permuted = TRUE, pars = "m")$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: ‘xergm’
Packages suggested but not available for checking:
  'vsn', 'DESeq2', 'pasilla'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Brundle.Rcheck/00install.out’ for details.
installed size is 29.7Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  27.6Mb
installed size is 94.6Mb
  sub-directories of 1Mb or more:
    libs  93.9Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is 19.6Mb
  sub-directories of 1Mb or more:
    libs  19.4Mb
Error(s) in re-building vignettes:
--- re-building ‘examples.Rmd’ using rmarkdown
Warning 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


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]="webshot17f0e554a7ebc.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot17f0e554a7ebc.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
--- failed re-building ‘examples.Rmd’

SUMMARY: processing the following file failed:
  ‘examples.Rmd’

Error: Vignette re-building failed.
Execution halted
File ‘cairoDevice/R/zzz.R’:
  .onLoad calls:
    message("R session is headless; GTK+ not initialized.")

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

No protocol specified
Running examples in ‘cairoDevice-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cairo
> ### Title: The Cairo Graphics Device
> ### Aliases: Cairo Cairo_pdf Cairo_ps Cairo_svg Cairo_png
> ### Keywords: device
> 
> ### ** Examples
> 
> Cairo()

(R:47634): Gdk-CRITICAL **: gdk_screen_get_width: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_width_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_height: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_height_mm: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:47634): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:47634): Gtk-CRITICAL **: gtk_window_set_default_size: assertion `width >= -1' failed

(R:47634): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:47634): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:47634): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

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

Traceback:
 1: Cairo()
An irrecoverable exception occurred. R is aborting now ...
Packages suggested but not available for checking:
  'GenomicRanges', 'IRanges', 'S4Vectors'
Package unavailable to check Rd xrefs: ‘GenomicRanges’
Package suggested but not available for checking: ‘limma’
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/3.6/cape.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   3.7Mb
Package unavailable to check Rd xrefs: ‘limma’
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 loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) : 
  there is no package called ‘GenomeInfoDbData’
Calls: stat.DESeq ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘CaRpools.Rmd’ using rmarkdown
Warning 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:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘CaRpools.Rmd’

SUMMARY: processing the following file failed:
  ‘CaRpools.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘cartograflow.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in normalizePath(f2) :
  path[1]="webshot87bf53b79c.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot87bf53b79c.png': No such file or directory
Quitting from lines 451-480 (cartograflow.Rmd) 
Error: processing vignette 'cartograflow.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘cartograflow.Rmd’

SUMMARY: processing the following file failed:
  ‘cartograflow.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs  10.3Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    data      1.2Mb
    extdata   1.1Mb
    libs      3.0Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.0Mb
Package suggested but not available for checking: ‘graph’
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.0Mb
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    extdata   9.2Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    data   3.2Mb
    doc    1.7Mb
    libs   5.9Mb
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/3.6/changepoint.np.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘pbdMPI’
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/3.6/ChaosGame.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘multtest’
Packages suggested but not available for checking:
  'GenomicInteractions', 'Gviz', 'countreg'
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Introduction.Rmd’

--- re-building ‘Visualising_Interactions.Rmd’ using rmarkdown
Warning 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'
--- failed re-building ‘Visualising_Interactions.Rmd’

SUMMARY: processing the following file failed:
  ‘Visualising_Interactions.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ComplexHeatmap’
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    data   1.8Mb
    libs   4.1Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   8.6Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CleanBSequences.Rcheck/00install.out’ for details.
installed size is 20.7Mb
  sub-directories of 1Mb or more:
    libs  19.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/clpAPI.Rcheck/00install.out’ for details.
Package required but not available: ‘IsoGene’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
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/3.6/clusterSim.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
Packages suggested but not available for checking:
  'SingleCellExperiment', 'SummarizedExperiment'
Error loading dataset 'sc_example':
   Error in .requirePackage(package) : 
    unable to find required package 'S4Vectors'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'moe430a.db'
Package unavailable to check Rd xrefs: ‘Biobase’
Error(s) in re-building vignettes:
  ...
--- re-building ‘clValid.Rnw’ using Sweave
Loading required package: cluster
Read 7 items
Loading required package: Biobase
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘Biobase’
Loading required package: RankAggreg
Error: processing vignette 'clValid.Rnw' failed with diagnostics:
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!
--- failed re-building ‘clValid.Rnw’

SUMMARY: processing the following file failed:
  ‘clValid.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages required but not available:
  'InteractionSet', 'GenomicInteractions',
  'BSgenome.Hsapiens.UCSC.hg19'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   3.3Mb
Namespaces in Imports field not imported from:
  ‘graphics’ ‘jsonlite’ ‘pander’ ‘rlang’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘Vignette.Rmd’ using rmarkdown
Warning 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: Epi
Quitting from lines 36-38 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [64s/64s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 3. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$pcc, 3), round(unlist(corr), 3)) isn't true.
  
  ── 4. Failure: the app results are reproduced using imager only (@test-reproduce
  all.equal(round(stats$moc, 3), round(unlist(corr), 3)) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 38 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 4 ]
  1. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#32) 
  2. Failure: the app results are reproduced faithfuly (@test-reproduce_app.R#35) 
  3. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#126) 
  4. Failure: the app results are reproduced using imager only (@test-reproduce_app.R#145) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc       2.6Mb
    extdata   2.1Mb
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   6.3Mb
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/3.6/colourvision.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [9s/11s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] 1
  
  $functi
  function (x)  .Primitive("sin")
  
  Error in summary.connection(connection) : invalid connection
  In addition: Warning message:
  In .Internal(gc(verbose, reset, full)) :
    closing unused connection 4 (<-localhost:11149)
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 128 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: ffexp parallel 2 (@test_ffexp.R#96) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 30.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    libs  28.7Mb
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  21.9Mb
Packages suggested but not available for checking:
  'inSilicoDb', 'mogene10sttranscriptcluster.db'
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/3.6/CompRandFld.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/CONDOP.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   11. pins::board_pin_store(...)
   13. pins:::board_pin_create.local(...)
   14. pins:::pin_registry_update(name = name, component = board$name)
   15. pins:::pin_registry_save_entries(entries, component)
   16. yaml::write_yaml(entries, pin_registry_config(component))
   17. base::file(file, "w", encoding = fileEncoding)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 22 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: tbl pin is created w/o error (@test-pins.R#16) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  call dbDisconnect() when finished working with a 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/3.6/ConsRank.Rcheck/00install.out’ for details.
installed size is 51.9Mb
  sub-directories of 1Mb or more:
    libs  50.7Mb
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/3.6/ConvergenceConcepts.Rcheck/00install.out’ for details.
Running examples in ‘ConvergenceConcepts-Ex.R’ failed
The error most likely occurred in:

> ### Name: investigate
> ### Title: Investigate examples and exercises from the paper
> ### Aliases: investigate
> ### Keywords: dplot iplot distribution htest
> 
> ### ** Examples
> 
> investigate()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: investigate ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
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/3.6/CoopGame.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/3.6/cops.Rcheck/00install.out’ for details.
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    R     2.1Mb
    doc   5.6Mb
Package suggested but not available for checking: ‘ProData’
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/3.6/corregp.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.8Mb
installed size is  9.9Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction_to_coveffectsplot.Rmd’ using rmarkdown
Warning 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 253-341 (introduction_to_coveffectsplot.Rmd) 
Error: processing vignette 'introduction_to_coveffectsplot.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction_to_coveffectsplot.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction_to_coveffectsplot.Rmd’

Error: Vignette re-building 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/3.6/CovTools.Rcheck/00install.out’ for details.
No protocol specified
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/cplexAPI.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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 399-421 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'AnnotationDbi', 'org.Hs.eg.db', 'clusterProfiler'
Error(s) in re-building vignettes:
--- re-building ‘case_study.Rmd’ using rmarkdown
Warning 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: R.oo
Loading required package: R.methodsS3
R.methodsS3 v1.7.1 (2016-02-15) successfully loaded. See ?R.methodsS3 for help.
R.oo v1.22.0 (2018-04-21) successfully loaded. See ?R.oo for help.

Attaching package: 'R.oo'

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

    getClasses, getMethods

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

    attach, detach, gc, load, save

R.utils v2.8.0 successfully loaded. See ?R.utils for help.

Attaching package: 'R.utils'

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

    timestamp

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

    cat, commandArgs, getOption, inherits, isOpen, nullfile,
    parse, warnings


Attaching package: 'igraph'

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

    hierarchy

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

    decompose, spectrum

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

    union

Quitting from lines 32-41 (case_study.Rmd) 
Error: processing vignette 'case_study.Rmd' failed with diagnostics:
there is no package called 'AnnotationDbi'
--- failed re-building ‘case_study.Rmd’

--- re-building ‘using_cRegulome.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Picking joint bandwidth of 0.0445
--- finished re-building ‘using_cRegulome.Rmd’

SUMMARY: processing the following file failed:
  ‘case_study.Rmd’

Error: Vignette re-building 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/3.6/crs.Rcheck/00install.out’ for details.
installed size is 25.1Mb
  sub-directories of 1Mb or more:
    libs  23.4Mb
installed size is 94.1Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs  90.1Mb
Package which this enhances but not available for checking: ‘pbdMPI’
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/3.6/cubing.Rcheck/00install.out’ for details.
Namespace in Imports field not imported from: ‘pspearman’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/curvHDR.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘RGtk2’
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    libs   4.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘cycling_data_analysis.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘cycling_data_analysis.Rmd’

SUMMARY: processing the following file failed:
  ‘cycling_data_analysis.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.1Mb
Running ‘testthat.R’ [30s/63s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: with_connection(con, decrypt(readRDS(con2), x))
  5: close(con)
  6: close.connection(con)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 272 SKIPPED: 2 FAILED: 1
  1. Error: non-file arguments (@test-encrypt-wrapper.R#71) 
  
  Error: testthat unit tests failed
  In addition: Warning message:
  In as.character(md$Built$R) :
    closing unused connection 3 (/var/folders/xn/m8dzdsgs7sg8q7jgflnqm8w80000gn/T//Rtmp8NbBae/file30d93392aefd)
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction.Rmd’

Error: Vignette re-building 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/3.6/dartR.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   3.4Mb
Package required but not available: ‘gWidgets2RGtk2’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending_dataMaid.Rmd’ using rmarkdown
Warning 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).
--- failed re-building ‘extending_dataMaid.Rmd’

SUMMARY: processing the following file failed:
  ‘extending_dataMaid.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘get_started.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘get_started.Rmd’

SUMMARY: processing the following file failed:
  ‘get_started.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [27s/54s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   1. base::eval.parent(Resource.load(descriptor))
   3. datapackage.r::Resource.load(descriptor)
   4. datapackage.r::dereferenceResourceDescriptor(descriptor, basePath)
   5. base::tryCatch(...)
   6. base:::tryCatchList(expr, classes, parentenv, handlers)
   7. base:::tryCatchOne(expr, names, parentenv, handlers[[1L]])
   8. value[[3L]](cond)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 247 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: remote 
  2. Error: remote 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 60.0Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  57.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘applications.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘applications.Rmd’

--- re-building ‘data.tree.Rmd’ using rmarkdown
Warning 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]="webshot157e81cd7762b.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot157e81cd7762b.png': No such file or directory
Quitting from lines 513-516 (data.tree.Rmd) 
Error: processing vignette 'data.tree.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘data.tree.Rmd’

SUMMARY: processing the following file failed:
  ‘data.tree.Rmd’

Error: Vignette re-building failed.
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.
Package required but not available: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'WGCNA', 'Biostrings', 'impute'
Error loading dataset 'Sample_ID_data':
   Error in .requirePackage(package) : 
    unable to find required package 'Biostrings'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.6Mb
Error(s) in re-building vignettes:
--- re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’ using rmarkdown
Warning 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


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
--- failed re-building ‘MultiObjectiveDecisionAnalysisinR.Rmd’

SUMMARY: processing the following file failed:
  ‘MultiObjectiveDecisionAnalysisinR.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘RC_units.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘RC_units.Rmd’

--- re-building ‘decoder.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘decoder.Rmd’

--- re-building ‘sjukhus.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘sjukhus.Rmd’

SUMMARY: processing the following file failed:
  ‘sjukhus.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 66.2Mb
  sub-directories of 1Mb or more:
    libs  63.6Mb
Packages unavailable to check Rd xrefs: ‘WGCNA’, ‘moduleColor’
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/3.6/depth.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   2.7Mb
Packages which this enhances but not available for checking:
  'gurobi', 'Rcplex', 'Rsymphony'
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  19.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DEVis.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   6.7Mb
installed size is 52.9Mb
  sub-directories of 1Mb or more:
    libs  52.5Mb
Package required but not available: ‘ALL’

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

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  11.4Mb
Running examples in ‘dgmb-Ex.R’ failed
The error most likely occurred in:

> ### Name: dgmb-package
> ### Title: Simulating Data for PLS Mode B Structural Models
> ### Aliases: dgmb-package dgmb
> ### Keywords: package
> 
> ### ** Examples
> 
> dgmbGui()
 --------------------------------------------------
| Simulating Data for PLS Mode B Structural Models |
| Version: 1.2                                     |
| Depends: abind, tcltk, MASS                      |
| Licence: GPL >= 2                                |
| System Requirements: tktable, BWidget            |
 --------------------------------------------------
Warning in tclRequire("BWidget") : Tcl package 'BWidget' not found
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "ComboBox".
Calls: dgmbGui -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  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/3.6/DGVM3D.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/3.6/DiceView.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/diffMeanVar.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/3.6/DiffusionRgqd.Rcheck/00install.out’ for details.
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc   5.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DiffusionRimp.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/3.6/DiffusionRjgqd.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc   5.6Mb
Error(s) in re-building vignettes:
--- re-building ‘Part_1_Introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_1_Introduction.Rmd’

--- re-building ‘Part_2_Transition_Densities.Rmd’ using rmarkdown
Warning 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 176-185 (Part_2_Transition_Densities.Rmd) 
Error: processing vignette 'Part_2_Transition_Densities.Rmd' failed with diagnostics:
there is no package called 'DiffusionRgqd'
--- failed re-building ‘Part_2_Transition_Densities.Rmd’

--- re-building ‘Part_3_Bivariate_Diffusions.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Part_3_Bivariate_Diffusions.Rmd’

--- re-building ‘DiffusionRjgqd_Paper.pdf.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_Paper.pdf.asis’

--- re-building ‘DiffusionRjgqd_RepMaterials.html.asis’ using asis
--- finished re-building ‘DiffusionRjgqd_RepMaterials.html.asis’

--- re-building ‘Part_4_Likelihood_Inference.html.asis’ using asis
--- finished re-building ‘Part_4_Likelihood_Inference.html.asis’

SUMMARY: processing the following file failed:
  ‘Part_2_Transition_Densities.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
Package suggested but not available for checking: ‘pcaL1’
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/3.6/Directional.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/3.6/directPA.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/3.6/DirichletReg.Rcheck/00install.out’ for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    libs  10.1Mb
Error(s) in re-building vignettes:
--- re-building ‘brt.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Loading required namespace: gbm
fitting final gbm model with a fixed number of 600 trees for Angaus
fitting final gbm model with a fixed number of 1800 trees for Angaus
gbm.simplify - version 2.9 
simplifying gbm.step model for Angaus with 11 predictors and 1000 observations 
original deviance = 0.6743(0.0269)
a fixed number of 5 drops will be tested
creating initial models...
dropping predictor: 1 2 3 4 5
processing final dropping of variables with full data
1-DSDam
2-SegLowFlow
3-USAvgT
4-SegTSeas
5-DSMaxSlope
fitting final gbm model with a fixed number of 1300 trees for Angaus
gbm.interactions - version 2.9
Cross tabulating interactions for gbm model with 11 predictors
1 2 3 4 5 6 7 8 9 10 
maximum value = 0.58


Error: processing vignette 'brt.Rnw' failed with diagnostics:
 chunk 12 (label = dismo-10) 
Error in library(gbm) : there is no package called ‘gbm’

--- failed re-building ‘brt.Rnw’

--- re-building ‘sdm.Rnw’ using Sweave
Loading required package: raster
Loading required package: sp
Checking rgeos availability: TRUE
Loading required namespace: XML
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
REQUEST_DENIED:Ayacucho+P.+Huamanga+Minas+Ckucho,Peru
Loading required namespace: rgeos
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in randomForest.default(m, y, ...) :
  The response has five or fewer unique values.  Are you sure you want to do regression?

Attaching package: ‘kernlab’

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

    buffer, rotated

Loading required namespace: gstat
Loading required namespace: deldir
--- finished re-building ‘sdm.Rnw’

SUMMARY: processing the following file failed:
  ‘brt.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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/3.6/DiversityOccupancy.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    include  16.2Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    R      1.6Mb
    data   2.1Mb
    libs   3.6Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DNLC.Rcheck/00install.out’ for details.
Running ‘runit.R’ [10s/14s]
  Running ‘testthat.R’ [0m/29m]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ✔  checking whether the namespace can be loaded with stated dependencies
     checking whether the namespace can be unloaded cleanly ...
    
  ✔  checking whether the namespace can be unloaded cleanly (441ms)
  
    
     checking loading without being on the library search path ...
    
  ✔  checking loading without being on the library search path (436ms)
  
    
     checking use of S3 registration ...
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 12.5Mb
  sub-directories of 1Mb or more:
    doc    2.8Mb
    libs   9.2Mb
Package unavailable to check Rd xrefs: ‘doMPI’
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/3.6/dpcR.Rcheck/00install.out’ for details.
installed size is 23.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/DRomics.Rcheck/00install.out’ for details.
Running examples in ‘drtmle-Ex.R’ failed
The error occurred in:


R version 3.6.0 beta (2019-04-15 r76395) -- "Planting of a Tree"
Copyright (C) 2019 The R Foundation for Statistical Computing
Platform: x86_64-apple-darwin15.6.0 (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 <- "drtmle"
> source(file.path(R.home("share"), "R", "examples-header.R"))
> options(warn = 1)
> library('drtmle')
Error: package or namespace load failed for ‘drtmle’ in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called ‘data.table’
Execution halted
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(drtmle)
  Error: package or namespace load failed for 'drtmle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'data.table'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_drtmle.Rmd’ using rmarkdown
Warning 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 385-393 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
package or namespace load failed for 'drtmle' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
 there is no package called 'data.table'
--- failed re-building ‘using_drtmle.Rmd’

SUMMARY: processing the following file failed:
  ‘using_drtmle.Rmd’

Error: Vignette re-building 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/3.6/drugCombo.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘userGuide.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in 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]="webshot219036569873.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot219036569873.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
--- failed re-building ‘userGuide.Rmd’

SUMMARY: processing the following file failed:
  ‘userGuide.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    appinformation   3.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Designing-33PC.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (Designing-33PC.Rmd) 
Error: processing vignette 'Designing-33PC.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Designing-33PC.Rmd’

SUMMARY: processing the following file failed:
  ‘Designing-33PC.Rmd’

Error: Vignette re-building 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/3.6/dti.Rcheck/00install.out’ for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.8Mb
installed size is 29.6Mb
  sub-directories of 1Mb or more:
    data   4.2Mb
    doc    1.7Mb
    libs  23.3Mb
Running ‘testthat.R’ [51s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
    6. base::loadNamespace(name)
    9. base::loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]])
   11. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   13. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   14. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   15. base:::withOneRestart(expr, restarts[[1L]])
   16. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 191 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Perform dimred dm_destiny 
  2. Error: Perform dimred dm_destiny 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    doc    1.5Mb
    libs   2.8Mb
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Package suggested but not available for checking: ‘dyndimred’
Package unavailable to check Rd xrefs: ‘dyndimred’
Running examples in ‘dynwrap-Ex.R’ failed
The error most likely occurred in:

> ### Name: add_dimred
> ### Title: Add or create a dimensionality reduction
> ### Aliases: add_dimred is_wrapper_with_dimred get_dimred
> ### Keywords: adapt_trajectory
> 
> ### ** Examples
> 
> dataset <- example_dataset
> dataset <- add_dimred(
+   dataset,
+   dyndimred::dimred_landmark_mds
+ )
Error in loadNamespace(name) : there is no package called ‘dyndimred’
Calls: add_dimred ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Running ‘testthat.R’ [53s/51s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   4. base::asNamespace(ns)
   5. base::getNamespace(ns)
   6. base::loadNamespace(name)
   7. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   8. base:::withOneRestart(expr, restarts[[1L]])
   9. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 918 | SKIPPED: 1 | WARNINGS: 0 | FAILED: 3 ]
  1. Error: (unknown) (@test-method_infer_trajectory.R#3) 
  2. Error: Testing add_dimred including calculation of dimred (@test-wrap_add_dimred.R#110) 
  3. Error: Test get_dimred (@test-wrap_add_dimred.R#278) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   3.7Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/edgeRun.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/3.6/edrGraphicalTools.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/3.6/eegkit.Rcheck/00install.out’ for details.
installed size is 68.7Mb
  sub-directories of 1Mb or more:
    libs  68.1Mb
Package suggested but not available for checking: ‘BiocStyle’
Error(s) in re-building vignettes:
--- re-building ‘EHRtemporalVariability.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Joining, by = "diagcode1"
Warning: Column `diagcode1` joining factor and character vector, coercing into character vector
# Missing values: 0 cases ( 0%)
# External causes codes: 0 cases ( 0%)
# V codes not mapped: 74330 cases ( 22.82%)
# Total ICD9-CM codes mapped: 146262 cases ( 44.9%)
# Unique ICD9-CM codes mapped: 3020
# Total PheWAS codes: 757
# ICD9 codes not mapped: 105180 cases ( 32.29%)
Quitting from lines 317-322 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘EHRtemporalVariability.Rmd’

SUMMARY: processing the following file failed:
  ‘EHRtemporalVariability.Rmd’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘elementR-Ex.R’ failed
The error most likely occurred in:

> ### Name: elementR_project
> ### Title: Object elementR_project
> ### Aliases: elementR_project
> 
> ### ** Examples
> 
> ## create a new elementR_repStandard object based on the "filePath" 
> ## from a folder containing sample replicate
> 
> filePath <- system.file("Example_Session", package="elementR")
> 
> exampleProject <- elementR_project$new(filePath)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: <Anonymous> ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Packages suggested but not available for checking:
  'hgu133plus2.db', 'lumi', 'GO.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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(zoo)

Attaching package: ‘zoo’

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

    as.Date, as.Date.numeric

> 
> data("Esch_Sure2010")
> data("qs_factor")
> 
> cinp            <- 150 # water consumption [m3/h]
> prec            <- Esch_Sure2010[1:1000,] # selecting just the first 1,000 rows
> 
> cinp.daily.file <- qs_factor
> 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 ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [13s/15s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  pandoc document conversion failed with error 127
  1: set_methods(methods_file) at testthat/test-eml2.R:25
  2: set_TextType(methods_file)
  3: to_docbook(file)
  4: pandoc_convert(basename(file), to = "docbook", output = normalizePath(docbook_file, 
         winslash = "/", mustWork = FALSE), options = "-s")
  5: stop("pandoc document conversion failed with error ", result, call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 83 SKIPPED: 5 WARNINGS: 3 FAILED: 2
  1. Error: set_method with additional input files (@test-additional-tests.R#43) 
  2. Error: we can do a complete eml construction (@test-eml2.R#25) 
  
  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/3.6/EMMIXcskew.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   3.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/empiricalFDR.DESeq2.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/emstreeR.Rcheck/00install.out’ for details.
Running examples in ‘eph-Ex.R’ failed
The error most likely occurred in:

> ### Name: get_poverty_lines
> ### Title: Descarga de canasta basica alimentaria y canasta basica total
> ### Aliases: get_poverty_lines
> 
> ### ** Examples
> 
> 
> canasta <- get_poverty_lines()
trying URL 'https://www.indec.gob.ar/ftp/cuadros/sociedad/serie_cba_cbt.xls'
Warning in utils::download.file(dataURL, destfile = temp, mode = "wb") :
  URL 'https://www.indec.gob.ar/ftp/cuadros/sociedad/serie_cba_cbt.xls': status was 'Couldn't connect to server'
Error in utils::download.file(dataURL, destfile = temp, mode = "wb") : 
  cannot open URL 'https://www.indec.gob.ar/ftp/cuadros/sociedad/serie_cba_cbt.xls'
Calls: get_poverty_lines -> <Anonymous>
Execution halted
Running ‘testthat.R’ [4s/157s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  
  trying URL 'https://www.indec.gob.ar/ftp/cuadros/sociedad/serie_cba_cbt.xls'
  ── 2. Error: test canasta (@test-get_poverty_lines.R#4)  ───────────────────────
  cannot open URL 'https://www.indec.gob.ar/ftp/cuadros/sociedad/serie_cba_cbt.xls'
  Backtrace:
   1. eph::get_poverty_lines()
   2. utils::download.file(dataURL, destfile = temp, mode = "wb")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 11 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 2 ]
  1. Error: nuevas bases (@test-get_microdata.R#18) 
  2. Error: test canasta (@test-get_poverty_lines.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epicontacts.Rmd’ using rmarkdown
Warning 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]="webshotb53a10875b16.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb53a10875b16.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
--- failed re-building ‘epicontacts.Rmd’

--- re-building ‘epicontacts_class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epicontacts_class.Rmd’

SUMMARY: processing the following file failed:
  ‘epicontacts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘epiflows-class.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘epiflows-class.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘EpiReport_Vignette.Rmd’ using rmarkdown
Warning 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 367-368 (EpiReport_Vignette.Rmd) 
Error: processing vignette 'EpiReport_Vignette.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
--- failed re-building ‘EpiReport_Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘EpiReport_Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  motor_param.cpp:257:5: warning: explicitly assigning value of variable of type 'arma::vec' (aka 'Col<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/episode.Rcheck/00install.out’ for details.
installed size is 12.3Mb
  sub-directories of 1Mb or more:
    libs  12.0Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   1.8Mb
Package required but not available: ‘rpanel’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Errors in running code in vignettes:
when running code in ‘ESEA.Rnw’
  ...

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

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

  When sourcing ‘ESEA.R’:
Error: there is no package called ‘graph’
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘ESEA.Rnw’ using Sweave
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

Loading required package: XML
Loading required package: parmigene

Error: processing vignette 'ESEA.Rnw' failed with diagnostics:
 chunk 11 
Error in loadNamespace(name) : there is no package called ‘graph’

--- failed re-building ‘ESEA.Rnw’

SUMMARY: processing the following file failed:
  ‘ESEA.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.7Mb
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/3.6/etasFLP.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/3.6/Evomorph.Rcheck/00install.out’ for details.
installed size is 22.9Mb
  sub-directories of 1Mb or more:
    libs  22.8Mb
installed size is 13.1Mb
  sub-directories of 1Mb or more:
    exiftool  13.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ExomeDepth.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/3.6/export.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Package suggested but not available for checking: ‘fable’
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   4.4Mb
Found the following significant warnings:
  Warning: ‘i’ is used uninitialized in this function [-Wuninitialized]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/fAsianOptions.Rcheck/00install.out’ for details.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   2.1Mb
installed size is 42.3Mb
  sub-directories of 1Mb or more:
    libs  42.1Mb
installed size is 17.8Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs  16.4Mb
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    libs   2.5Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    libs  18.1Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs      6.9Mb
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/3.6/FastRWeb.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'DESeq2', 'destiny'
Error(s) in re-building vignettes:
  ...
--- re-building ‘FateID.Rmd’ using rmarkdown
Warning 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 141-142 (FateID.Rmd) 
Error: processing vignette 'FateID.Rmd' failed with diagnostics:
there is no package called 'destiny'
--- failed re-building ‘FateID.Rmd’

SUMMARY: processing the following file failed:
  ‘FateID.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
installed size is 39.9Mb
  sub-directories of 1Mb or more:
    doc    2.9Mb
    libs  36.3Mb
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/3.6/fdaPDE.Rcheck/00install.out’ for details.
installed size is 23.9Mb
  sub-directories of 1Mb or more:
    libs  23.6Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   8.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning 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: rainbow
Loading required package: MASS
Loading required package: pcaPP
Loading required package: RCurl
Loading required package: bitops

Execution halted
Running ‘test-as-dgCMatrix.R’ [2s/2s]
  Running ‘test-empty_array.R’ [2s/2s]
  Running ‘test-existence_collision.R’ [2s/2s]
  Running ‘test-hash.mapping.R’ [2s/2s]
  Running ‘test-hashing.R’ [2s/2s]
Running the tests in ‘tests/test-hashing.R’ failed.
Last 13 lines of output:
  +     if (class(e)[1] != "std::invalid_argument") stop(e)
  +     if (conditionMessage(e) != "Failed to find the column:PlAnT") stop(e)
  +   })
  +   
  +   m <- hashed.model.matrix(~ Plant:Type:Treatment, CO2, create.mapping = TRUE, signed.hash = TRUE)
  +   map <- hash.mapping(m)
  +   map <- map[grepl("\\w+:\\w+:\\w+", names(map))]
  +   checkTrue(all(hashed.interaction.value(names(map)) %% (2^18) + 1== map),
  +             "The hashed.interaction.value gives inconsistent result of hashed.model.matrix")
  + }
  Loading required package: RUnit
  Error in .hashed.model.matrix.dataframe(tf, data, hash.size, transpose,  : 
    c++ exception (unknown reason)
  Calls: tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
  Execution halted
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/3.6/feature.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [1s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(felp)
  
  Attaching package: 'felp'
  
  The following object is masked from 'package:utils':
  
      ?
  
  > 
  > test_check("felp")
  Error: pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Execution halted
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
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/3.6/FieldSim.Rcheck/00install.out’ for details.
Package required and available but unsuitable version: ‘EML’

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/3.6/fingerPro.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘quick_charts.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Warning in normalizePath(f2) :
  path[1]="webshot114e76fe61b6d.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot114e76fe61b6d.png': No such file or directory
Quitting from lines 125-134 (quick_charts.Rmd) 
Error: processing vignette 'quick_charts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘quick_charts.Rmd’

SUMMARY: processing the following file failed:
  ‘quick_charts.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘lifeExpectancy.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘lifeExpectancy.Rmd’

--- re-building ‘selectIndicatorsRedRed.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘selectIndicatorsRedRed.Rmd’

SUMMARY: processing the following file failed:
  ‘lifeExpectancy.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   2.5Mb
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/3.6/fit4NM.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13272): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
'library' or 'require' calls to packages already attached by Depends:
  ‘RGtk2’ ‘cairoDevice’ ‘gWidgets’ ‘gWidgetsRGtk2’ ‘tcltk’ ‘tkrplot’
  Please remove these calls from your code.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13280): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13288): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13296): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13356): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13364): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13372): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13380): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:13394): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Running examples in ‘fit4NM-Ex.R’ failed
The error most likely occurred in:

> ### Name: fit4NM
> ### Title: Platform for NONMEM
> ### Aliases: fit4NM
> ### Keywords: utilities
> 
> ### ** Examples
> 
> fit4NM()

(R:13419): GLib-GObject-WARNING **: invalid (NULL) pointer instance

(R:13419): GLib-GObject-CRITICAL **: g_signal_connect_data: assertion `G_TYPE_CHECK_INSTANCE (instance)' failed

(R:13419): Gtk-WARNING **: Screen for GtkWindow not set; you must always set
a screen for a GtkWindow before using the window

(R:13419): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:13419): Gdk-CRITICAL **: gdk_colormap_get_visual: assertion `GDK_IS_COLORMAP (colormap)' failed

(R:13419): Gdk-CRITICAL **: gdk_screen_get_default_colormap: assertion `GDK_IS_SCREEN (screen)' failed

(R:13419): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:13419): Gdk-CRITICAL **: gdk_screen_get_root_window: assertion `GDK_IS_SCREEN (screen)' failed

(R:13419): Gdk-CRITICAL **: gdk_window_new: assertion `GDK_IS_WINDOW (parent)' failed

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

Traceback:
 1: .RGtkCall("S_gtk_widget_show", object, PACKAGE = "RGtk2")
 2: method(obj, ...)
 3: window$Show()
 4: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 5: .gwindow(toolkit, title, visible, width, height, parent, handler,     action, ...)
 6: gwindow("GUI for NONMEM", width = 850, height = 300)
 7: fit4NM()
An irrecoverable exception occurred. R is aborting now ...
Error(s) in re-building vignettes:
  ...
--- re-building ‘fitbitScraper-examples.Rmd’ using rmarkdown
Warning in engine$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
--- failed re-building ‘fitbitScraper-examples.Rmd’

SUMMARY: processing the following file failed:
  ‘fitbitScraper-examples.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   2.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/float.Rcheck/00install.out’ for details.
installed size is 15.0Mb
  sub-directories of 1Mb or more:
    libs  14.7Mb
installed size is 48.0Mb
  sub-directories of 1Mb or more:
    libs  46.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontHind.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Using_fontHind.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_fontHind.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Using_fontMPlus.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Using_fontMPlus.Rmd’

SUMMARY: processing the following file failed:
  ‘Using_fontMPlus.Rmd’

Error: Vignette re-building 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/3.6/foodweb.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/3.6/forestFloor.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/3.6/ForImp.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘formattable-data-frame.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘formattable-data-frame.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘formattable-data-frame.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Introduction-to-formulaic.Rmd’ using rmarkdown
Warning 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 127-132 (Introduction-to-formulaic.Rmd) 
Error: processing vignette 'Introduction-to-formulaic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Introduction-to-formulaic.Rmd’

SUMMARY: processing the following file failed:
  ‘Introduction-to-formulaic.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘seasonal’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    help   1.6Mb
    libs   4.5Mb
Package required but not available: ‘pkgfilecache’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   6.0Mb
Found the following significant warnings:
  c_hd_mf.cpp:157:12: warning: explicitly assigning value of variable of type 'Eigen::VectorXd' (aka 'Matrix<double, Dynamic, 1>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/FRegSigCom.Rcheck/00install.out’ for details.
installed size is 61.7Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs  59.9Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs   6.0Mb
Package unavailable to check Rd xrefs: ‘frm’
installed size is 40.5Mb
  sub-directories of 1Mb or more:
    libs  40.0Mb
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/3.6/frontiles.Rcheck/00install.out’ for details.
Package required but not available: ‘pkgfilecache’

Package required and available but unsuitable version: ‘freesurferformats’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘RTCGA.rnaseq’
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    libs   9.5Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    libs  14.5Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Package required but not available: ‘breastCancerVDX’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.6Mb
  sub-directories of 1Mb or more:
    libs  25.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘futureheatwaves.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘futureheatwaves.Rmd’

--- re-building ‘starting_from_netcdf.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘starting_from_netcdf.Rmd’

SUMMARY: processing the following file failed:
  ‘futureheatwaves.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘WGCNA’
Error(s) in re-building vignettes:
--- re-building ‘chart_themes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Please send questions to cbioportal@googlegroups.com
Quitting from lines 48-58 (chart_themes.Rmd) 
Error: processing vignette 'chart_themes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘chart_themes.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
g3viz: visualizing gene/genome/gentics data for fun.
Any questions, please send emails to <g3viz.group@gmail.com>
Quitting from lines 103-114 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘chart_themes.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘ArrayBin’
Package suggested but not available for checking: ‘DAAGbio’
Package which this enhances but not available for checking: ‘doMPI’
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    doc    1.7Mb
    libs   3.9Mb
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   7.5Mb
installed size is 79.9Mb
  sub-directories of 1Mb or more:
    libs  79.5Mb
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    extdata   1.6Mb
    libs     55.4Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  14.9Mb
Packages suggested but not available for checking:
  'classGraph', 'graph', 'Rgraphviz'
installed size is 170.2Mb
  sub-directories of 1Mb or more:
    L8NY18    2.2Mb
    libs    166.7Mb
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/3.6/gdimap.Rcheck/00install.out’ for details.
installed size is 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.3Mb
Running ‘testthat.R’ [6s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > test_check("genBaRcode")
  ── 1. Error: (unknown) (@test_raw_data_functions.R#3)  ─────────────────────────
  package 'GenomeInfoDb' could not be loaded
  Backtrace:
   1. base::library(ShortRead)
   2. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
   3. base::library(...)
   4. base::.getRequiredPackages2(pkgInfo, quietly = quietly)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 17 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: (unknown) (@test_raw_data_functions.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘genBaRcode_GUI_Vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘genBaRcode_GUI_Vignette.Rmd’

--- re-building ‘genBaRcode_Vignette.Rmd’ using rmarkdown
Warning 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 155-176 (genBaRcode_Vignette.Rmd) 
Error: processing vignette 'genBaRcode_Vignette.Rmd' failed with diagnostics:
there is no package called 'GenomeInfoDbData'
--- failed re-building ‘genBaRcode_Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘genBaRcode_Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [9s/9s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to baseline..."
  [1] "clustering genes from baseline samples normalized to mean..."
  [1] "clustering genes from baseline samples normalized to controls..."
  [1] "clustering genes from all samples normalized to mean..."
  [1] "clustering genes from all samples normalized to controls..."
  [1] "clustering genes from all samples normalized to baseline..."
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 134 | SKIPPED: 0 | WARNINGS: 2 | FAILED: 2 ]
  1. Error: genModelResults outputs correctly for one comparison (@test_genModelResults.R#64) 
  2. Error: genModelResults outputs correctly for multiple comparisons (@test_genModelResults.R#85) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
Packages suggested but not available for checking: 'lfa', 'snpStats'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/geno2proteo.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'KEGG.db', 'reactome.db', 'AnnotationDbi'
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/3.6/gensphere.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   2.8Mb
    libs   4.8Mb
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/3.6/geoelectrics.Rcheck/00install.out’ for details.
Output for data("sinkhole", package = "geoelectrics"):
  Warning messages:
  1: In rgl.init(initValue, onlyNULL) : RGL: unable to open X11 display
  2: 'rgl_init' failed, running with rgl.useNULL = TRUE
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    help   1.3Mb
    libs   4.0Mb
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    R         8.8Mb
    extdata   1.5Mb
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/3.6/geomorph.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   4.9Mb
Packages suggested but not available for checking: 'DESeq2', 'S4Vectors'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Running ‘testthat.R’ [33s/32s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(getCRUCLdata)
  > 
  > test_check("getCRUCLdata")
  ── 1. Failure: cache directory is created if necessary (@test_caching.R#29)  ───
  dir.exists(manage_cache$cache_path_get()) isn't true.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 34 | SKIPPED: 23 | WARNINGS: 1 | FAILED: 1 ]
  1. Failure: cache directory is created if necessary (@test_caching.R#29) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: ‘RGtk2’
Error(s) in re-building vignettes:
  ...
--- re-building ‘IntroductionToGFD.Rmd’ using rmarkdown
Warning 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'
--- failed re-building ‘IntroductionToGFD.Rmd’

SUMMARY: processing the following file failed:
  ‘IntroductionToGFD.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GFORCE.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GGEBiplotGUI.Rcheck/00install.out’ for details.
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 "toplevel".
Calls: GGEBiplot ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Running ‘testthat.R’ [3s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Missing values detected: (3%)
  Switching to 'nipals' method.
  Missing values detected: (3%)
  Switching to 'nipals' method.
  ── 1. Failure: rgl works (@test_gge.R#162)  ────────────────────────────────────
  `{ ... }` produced warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 14 SKIPPED: 0 FAILED: 1
  1. Failure: rgl works (@test_gge.R#162) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 20.6Mb
  sub-directories of 1Mb or more:
    help   1.1Mb
    libs  18.7Mb
Error(s) in re-building vignettes:
--- re-building ‘ggPredict.Rmd’ using rmarkdown
Warning 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

Attaching package: 'ggiraphExtra'

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

    addLabelDf, getMapping

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
--- failed re-building ‘ggPredict.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
Loading required package: ggiraph
Loading required package: ggiraphExtra
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot8a65240e95b5.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot8a65240e95b5.png': No such file or directory
Quitting from lines 28-33 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following files failed:
  ‘ggPredict.Rmd’ ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘gglogo-alphabet.Rmd’ using rmarkdown
Warning 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 45-52 (gglogo-alphabet.Rmd) 
Error: processing vignette 'gglogo-alphabet.Rmd' failed with diagnostics:
replacement has 1 row, data has 0
--- failed re-building ‘gglogo-alphabet.Rmd’

SUMMARY: processing the following file failed:
  ‘gglogo-alphabet.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘extending-ggplot2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘extending-ggplot2.Rmd’

--- re-building ‘ggplot2-specs.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ggplot2-specs.Rmd’

--- re-building ‘profiling.Rmd’ using rmarkdown
Warning 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 22-32 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘profiling.Rmd’

SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   2.2Mb
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: Matrix
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 185-186 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
Packages suggested but not available for checking:
  'BSgenome.Hsapiens.UCSC.hg18.masked',
  'BSgenome.Hsapiens.UCSC.hg19.masked'
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 41.8Mb
  sub-directories of 1Mb or more:
    libs  40.7Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    libs   6.6Mb
installed size is 40.9Mb
  sub-directories of 1Mb or more:
    libs  40.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rnw’ using knitr
--- finished re-building ‘intro.Rnw’

--- re-building ‘parallel.Rnw’ using knitr

Execution halted
SUMMARY: processing the following file failed:
  ‘parallel.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 43.8Mb
  sub-directories of 1Mb or more:
    libs  42.9Mb
installed size is 62.1Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  59.8Mb
glmulti,character-character-ANY-ANY: no visible global function
  definition for ‘regsubsets’
Undefined global functions or variables:
  regsubsets
Running examples in ‘glue-Ex.R’ failed
The error most likely occurred in:

> ### Name: glue_sql
> ### Title: Interpolate strings with SQL escaping
> ### Aliases: glue_sql glue_data_sql
> 
> ### ** Examples
> 
> con <- DBI::dbConnect(RSQLite::SQLite(), ":memory:")
Error in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]) : 
  there is no package called ‘digest’
Calls: <Anonymous> ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Packages suggested but not available for checking: 'graph', 'mutoss'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GMMAT.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/3.6/gMOIP.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Evaluation.cpp:173:9: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to true [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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.
Package required but not available: ‘WGCNA’

Package suggested but not available for checking: ‘WGCNA’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
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/3.6/GPGame.Rcheck/00install.out’ for details.
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    libs   5.1Mb
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/3.6/GPoM.FDLyapu.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/3.6/GPoM.Rcheck/00install.out’ for details.
Running examples in ‘gprofiler2-Ex.R’ failed
The error most likely occurred in:

> ### Name: gconvert
> ### Title: Gene ID conversion.
> ### Aliases: gconvert
> 
> ### ** Examples
> 
> gconvert(c("POU5F1", "SOX2", "NANOG"), organism = "hsapiens", target="AFFY_HG_U133_PLUS_2")
Error in function (type, msg, asError = TRUE)  : 
  Failed to connect to biit.cs.ut.ee port 80: Operation timed out
Calls: gconvert -> <Anonymous> -> <Anonymous> -> fun
Execution halted
installed size is 48.4Mb
  sub-directories of 1Mb or more:
    libs  45.9Mb
Running ‘testthat.R’ [68s/77s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 3096 | SKIPPED: 309 | WARNINGS: 0 | FAILED: 25 ]
  1. Error: gpuMatrix Double Precision Matrix-Vector multiplication (@test_gpuMatrix_algebra.R#840) 
  2. Error: gpuMatrix Integer Precision Sum (@test_gpuMatrix_row_col.R#41) 
  3. Error: gpuMatrix Double Precision Sum (@test_gpuMatrix_row_col.R#67) 
  4. Error: gpuMatrix Double Precision Block Sum (@test_gpuMatrix_row_col.R#400) 
  5. Error: gpuVector Double precision tcrossprod (@test_gpuVector_algebra.R#607) 
  6. Error: Switching GPUs vclMatrix Double Precision Matrix Multiplication (@test_switch_gpu_vclMatrix_algebra.R#480) 
  7. Error: Switching GPUs vclMatrix Double Precision Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#507) 
  8. Error: Switching GPUs vclMatrix Double Precision Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#535) 
  9. Error: Switching GPUs vclMatrix Double Precision Unary Scalar Matrix Subtraction (@test_switch_gpu_vclMatrix_algebra.R#567) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 27.7Mb
  sub-directories of 1Mb or more:
    R  27.6Mb
Running ‘testthat.R’ [63s/138s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  > library(gqlr)
  > 
  > test_check("gqlr")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 450 SKIPPED: 0 FAILED: 0
  Execution halted
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    libs  11.6Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    help   2.4Mb
    libs   2.7Mb
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/3.6/graphscan.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.1Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Found the following significant warnings:
  Warning: package ‘edgeR’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/GSAgm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘impute’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gsl.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [0s/1s]
Running the tests in ‘tests/testthat.R’ failed.
Complete output:
  > library(testthat)
  Error: package or namespace load failed for 'testthat' in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]):
   there is no package called 'rlang'
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘profiling.Rmd’ using rmarkdown
Warning 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 22-34 (profiling.Rmd) 
Error: processing vignette 'profiling.Rmd' failed with diagnostics:
package or namespace load failed for 'ggplot2' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'rlang'
--- failed re-building ‘profiling.Rmd’

SUMMARY: processing the following file failed:
  ‘profiling.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘interval’
Error(s) in re-building vignettes:
--- re-building ‘gunsales.Rmd’ using rmarkdown
Warning 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: 13995 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpZhJtlI/x1336a159a99349/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/3.6/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/3.6/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  0x1251da579
#1  0x1251d9945
#2  0x7fff9ae44529
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.
--- failed re-building ‘gunsales.Rmd’

SUMMARY: processing the following file failed:
  ‘gunsales.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘run-tests.R’ [1s/1s]
Running the tests in ‘tests/run-tests.R’ failed.
Last 13 lines of output:
  > f <- Filter(function(x) !grepl("html", x), f)
  > 
  > sapply(f, function(i) {
  +   message("testing ", i)
  +   source(i)
  + })
  testing /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/gWidgets2/tests/button.R
  Loading required package: gWidgets2RGtk2
  Loading required package: memoise
  Loading required package: RGtk2
  No protocol specified
  R session is headless; GTK+ not initialized.
  Error in guiToolkit() : Can't load RGtk2
  Calls: sapply ... withVisible -> eval -> eval -> gwindow -> guiToolkit
  Execution halted
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    libs   3.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/gwsem.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/h5.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘overview.Rmd’ using rmarkdown
Warning 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 40-43 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [1s/58s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > 
  > test_check("hail")
  ── 1. Error: hail_hydra works (@test.R#4)  ─────────────────────────────────────
  cannot open the connection to 'https://or.water.usgs.gov/precip/walmart_ecoroof.rain'
  1: hail_hydra("Walmart Eco Roof") at testthat/test.R:4
  2: hydra_base(station_data$urls, station_data$stations)
  3: readLines(url)
  4: file(con, "r")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 1 SKIPPED: 0 FAILED: 1
  1. Error: hail_hydra works (@test.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Basic_use.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Basic_use.Rmd’

SUMMARY: processing the following file failed:
  ‘Basic_use.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.3Mb
  sub-directories of 1Mb or more:
    libs  18.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hchinamap.Rmd’ using rmarkdown
Warning 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://czxb.github.io/br/chinadf.rda'
Content type 'application/octet-stream' length 3992 bytes
==================================================
downloaded 3992 bytes

Quitting from lines 50-58 (hchinamap.Rmd) 
Error: processing vignette 'hchinamap.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hchinamap.Rmd’

SUMMARY: processing the following file failed:
  ‘hchinamap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.3Mb
Error(s) in re-building vignettes:
--- re-building ‘heatmaply.Rmd’ using rmarkdown
Warning 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: plotly
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

Loading required package: viridis
Loading required package: viridisLite

======================
Welcome to heatmaply version 0.16.0

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
--- failed re-building ‘heatmaply.Rmd’

SUMMARY: processing the following file failed:
  ‘heatmaply.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'rgl', 'FRB'
Error(s) in re-building vignettes:
--- re-building ‘authentication.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘authentication.Rmd’

--- re-building ‘geocoder.Rmd’ using rmarkdown
Warning 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 51-58 (geocoder.Rmd) 
Error: processing vignette 'geocoder.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘geocoder.Rmd’

--- re-building ‘routing.Rmd’ using rmarkdown
Warning 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 40-48 (routing.Rmd) 
Error: processing vignette 'routing.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘routing.Rmd’

--- re-building ‘traffic.Rmd’ using rmarkdown
Warning 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 44-52 (traffic.Rmd) 
Error: processing vignette 'traffic.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘traffic.Rmd’

--- re-building ‘weather.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 52-59 (weather.Rmd) 
Error: processing vignette 'weather.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘weather.Rmd’

SUMMARY: processing the following files failed:
  ‘geocoder.Rmd’ ‘routing.Rmd’ ‘traffic.Rmd’ ‘weather.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘synbreed’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HeritSeq.Rcheck/00install.out’ for details.
installed size is 20.4Mb
  sub-directories of 1Mb or more:
    doc    4.6Mb
    libs  15.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hetGP_vignette.Rnw’ using knitr

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/3.6/hgam.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HiCfeat.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HierO.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    data   5.5Mb
    libs   1.2Mb
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    highlight   1.0Mb
    libs        8.0Mb
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/3.6/hiPOD.Rcheck/00install.out’ for details.
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    data   1.0Mb
    libs   5.2Mb
Package suggested but not available for checking: ‘trackr’
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/3.6/HiveR.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   3.5Mb
    libs   3.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/hoardeR.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'iheatmapr', 'ropls'
Error(s) in re-building vignettes:
  ...
--- re-building ‘simulating-data.Rmd’ using rmarkdown
Warning 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 25-31 (simulating-data.Rmd) 
Error: processing vignette 'simulating-data.Rmd' failed with diagnostics:
there is no package called 'ropls'
--- failed re-building ‘simulating-data.Rmd’

SUMMARY: processing the following file failed:
  ‘simulating-data.Rmd’

Error: Vignette re-building 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/3.6/homals.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘hpackedbubble.Rmd’ using rmarkdown
Warning 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 35-49 (hpackedbubble.Rmd) 
Error: processing vignette 'hpackedbubble.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hpackedbubble.Rmd’

SUMMARY: processing the following file failed:
  ‘hpackedbubble.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
File ‘hpa/libs/hpa.so’:
  Found ‘_printf’, possibly from ‘printf’ (C)
    Objects: ‘hpaBinary.o’, ‘hpaML.o’, ‘hpaSelection.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:
  'RGtk2', 'cairoDevice', 'RGtk2Extras'
Found the following significant warnings:
  sar.cpp:210:32: warning: explicitly assigning value of variable of type 'arma::sp_mat' (aka 'SpMat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/HSAR.Rcheck/00install.out’ for details.
installed size is 48.9Mb
  sub-directories of 1Mb or more:
    libs  48.5Mb
Running ‘testthat.R’ [52s/52s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
   18. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   20. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   22. base::loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]])
   23. base::withRestarts(stop(cond), retry_loadNamespace = function() NULL)
   24. base:::withOneRestart(expr, restarts[[1L]])
   25. base:::doWithOneRestart(return(expr), restart)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 102 | SKIPPED: 18 | WARNINGS: 3 | FAILED: 3 ]
  1. Error: DESeq2_l2fc runs with default params (@test-DESeq2_l2fc.R#2) 
  2. Error: DESeq2_l2fc runs with sparsity_apply=heavy (@test-DESeq2_l2fc.R#15) 
  3. Error: HRSIP runs with default (@test-HRSIP.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
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/3.6/HUM.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    dict   1.5Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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 161-165 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘hwordcloud.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-53 (hwordcloud.Rmd) 
Error: processing vignette 'hwordcloud.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘hwordcloud.Rmd’

SUMMARY: processing the following file failed:
  ‘hwordcloud.Rmd’

Error: Vignette re-building 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/3.6/hyper.fit.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘flowCore’
Error loading dataset 'Samusik_01_subset':
   Error in .requirePackage(package) : 
    unable to find required package 'flowCore'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION 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/3.6/hypervolume.Rcheck/00install.out’ for details.
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   3.0Mb
    libs   4.5Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘ibmsunburst.Rmd’ using rmarkdown
Warning 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 25-37 (ibmsunburst.Rmd) 
Error: processing vignette 'ibmsunburst.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘ibmsunburst.Rmd’

SUMMARY: processing the following file failed:
  ‘ibmsunburst.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ICAMS.Rcheck/00install.out’ for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘example.Rmd’ using rmarkdown
Warning 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 84-88 (example.Rmd) 
Error: processing vignette 'example.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘example.Rmd’

SUMMARY: processing the following file failed:
  ‘example.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    data   1.4Mb
    libs   5.9Mb
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  15.3Mb
Package suggested but not available for checking: ‘mixAK’
Running examples in ‘iClick-Ex.R’ failed
The error most likely occurred in:

> ### Name: iClick.ARIMA
> ### Title: iClick GUI for ARIMA
> ### Aliases: iClick.ARIMA
> 
> ### ** Examples
> 
> 
> ##External data
> data("world20")
> y=na.omit(diff(log(world20[,1])))
> 
> ## Simulation data
> #dat=rnorm(200,5,1)
> #y=ts(dat, start = c(1970, 1), frequency = 12)
> 
> iClick.ARIMA(y)
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: iClick.ARIMA ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
Found the following significant warnings:
  RccpSource_.cpp:978:54: warning: explicitly assigning value of variable of type 'Rcpp::NumericVector' (aka 'Vector<14>') to itself [-Wself-assign-overloaded]
  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/3.6/icosa.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   1.4Mb
    libs      2.2Mb
installed size is 64.9Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  63.2Mb
installed size is 29.2Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs  27.7Mb
Error(s) in re-building vignettes:
--- re-building ‘model_details.Rmd’ using rmarkdown
Warning 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 25-32 (model_details.Rmd) 
Error: processing vignette 'model_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘model_details.Rmd’

--- re-building ‘parameter_details.Rmd’ using rmarkdown
Warning 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 24-31 (parameter_details.Rmd) 
Error: processing vignette 'parameter_details.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘parameter_details.Rmd’

--- re-building ‘resources.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘resources.Rmd’

SUMMARY: processing the following files failed:
  ‘model_details.Rmd’ ‘parameter_details.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    help   1.2Mb
    libs  14.9Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.2Mb
installed size is 29.4Mb
  sub-directories of 1Mb or more:
    data      1.4Mb
    doc       5.3Mb
    include   2.8Mb
    libs     18.3Mb
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘getstarted.Rmd’ using rmarkdown
Warning 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 87-89 (getstarted.Rmd) 
Error: processing vignette 'getstarted.Rmd' failed with diagnostics:
cannot open the connection to 'https://dane.imgw.pl/data/dane_pomiarowo_obserwacyjne/dane_hydrologiczne/miesieczne/mies_info.txt'
--- failed re-building ‘getstarted.Rmd’

SUMMARY: processing the following file failed:
  ‘getstarted.Rmd’

Error: Vignette re-building failed.
Execution halted
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:22:62: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  ImmigrateCpp.cpp:32:62: 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/3.6/Immigrate.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [4s/4s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                AminusB               CminusD AminusB.minus.CminusD 
           0.0005571069         -0.0005571069          0.0011142137 
  
  $var
                AminusB               CminusD AminusB.minus.CminusD 
             0.01610192            0.01610192            0.06440770 
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 12 SKIPPED: 0 WARNINGS: 9 FAILED: 3
  1. Error: (unknown) (@test_createANDundoIMRMCdf.R#26) 
  2. Error: (unknown) (@test_doIMRMC.R#25) 
  3. Error: (unknown) (@test_doIMRMCfromFile.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    libs   4.2Mb
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: 93537 Trace/BPT trap: 5       /Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/x13binary/bin/x13ashtml /tmp/RtmpXHYcnG/x1316d59200b633d/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/3.6/x13binary/bin/x13ashtml /tmp/RtmpXHYcnG/x1316d59200b633d/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/3.6/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/3.6/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  0x1248ae579
#1  0x1248ad945
#2  0x7fff994ee529
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 11.5Mb
  sub-directories of 1Mb or more:
    libs  11.2Mb
Packages suggested but not available for checking:
  'MLP', 'org.Hs.eg.db', 'a4Base'
Error(s) in re-building vignettes:
--- re-building ‘IntGraphTutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: dplyr

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Loading required package: DiagrammeR
Loading required package: DiagrammeRsvg
Loading required package: rsvg
Loading required package: gtools
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]="webshot15a63ac4ea79.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot15a63ac4ea79.png': No such file or directory
Quitting from lines 32-34 (IntGraphTutorial.Rmd) 
Error: processing vignette 'IntGraphTutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘IntGraphTutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘IntGraphTutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘apeglm’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 26.9Mb
  sub-directories of 1Mb or more:
    libs  26.7Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   8.2Mb
.nndsvd.internal: no visible global function definition for ‘runif’
nmf.mnnals: no visible global function definition for ‘runif’
nmf.opt.k: no visible global function definition for ‘flush.console’
nmf.opt.k: no visible global function definition for ‘points’
nmf.opt.k: no visible global function definition for ‘lines’
nmf.opt.k: no visible global function definition for ‘mtext’
Undefined global functions or variables:
  flush.console lines mtext points runif
Consider adding
  importFrom("graphics", "lines", "mtext", "points")
  importFrom("stats", "runif")
  importFrom("utils", "flush.console")
to your NAMESPACE file.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.4Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ionflows.Rcheck/00install.out’ for details.
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
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
Error(s) in re-building vignettes:
--- re-building ‘getting-started-with-irg.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
ndvi                    package:irg                    R Documentation

_R_a_w _N_D_V_I _T_i_m_e _S_e_r_i_e_s

_D_e_s_c_r_i_p_t_i_o_n:

     A data.table containing NDVI samples for ten points over ten years
     (2002-2012).

_F_o_r_m_a_t:

     A data.table with 2530 rows and 5 variables:

        • id - individual identifier

        • yr - year of sample

        • DayOfYear - julian day/day of year of sample

        • NDVI - sampled value

        • SummaryQA - Summary quality assessment value

     SummaryQA details:

        • 0 - Good data, use with confidence

        • 1 - Marginal data, useful but look at detailed QA for more
          information

        • 2 - Pixel covered with snow/ice

        • 3 - Pixel is cloudy

_E_x_a_m_p_l_e_s:

     # Load data.table
     library(data.table)
     
     # Read example data
     ndvi <- fread(system.file("extdata", "ndvi.csv", package = "irg"))
     

Quitting from lines 99-153 (getting-started-with-irg.Rmd) 
Error: processing vignette 'getting-started-with-irg.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started-with-irg.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started-with-irg.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'pcalg', 'Rgraphviz'
Error(s) in re-building vignettes:
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning 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: pkgmaker
Loading required package: registry

Attaching package: 'pkgmaker'

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

    isFALSE

Loading required package: rngtools
Loading required package: cluster
# NOTE - CRAN check detected: limiting maximum number of cores [2/8]
NMF - BioConductor layer [NO: missing Biobase] | Shared memory capabilities [OK] | Cores 2/2 | CRAN check
  To enable the Bioconductor layer, try: install.extras('
NMF
') [with Bioconductor repository enabled]
Quitting from lines 94-99 (vignette.Rmd) 
Error: processing vignette 'vignette.Rmd' failed with diagnostics:
there is no package called 'pcalg'
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.0Mb
  sub-directories of 1Mb or more:
    art_profiles   1.5Mb
    libs          14.8Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/JFE.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.0Mb
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    data   1.1Mb
    libs   5.6Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.3Mb
    libs   3.4Mb
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/3.6/jomo.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   3.7Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    libs  15.7Mb
Missing or unexported object: ‘tidyr::unnest_legacy’
Package required but not available: ‘pbdMPI’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
installed size is 18.4Mb
  sub-directories of 1Mb or more:
    doc    1.3Mb
    libs  16.6Mb
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/3.6/kernhaz.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘org.Hs.eg.db’
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/3.6/KernSmoothIRT.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/kmcudaR.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/3.6/kml3d.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/3.6/kml.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/3.6/kmlShape.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   4.4Mb
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   3.3Mb
Error(s) in re-building vignettes:
--- re-building ‘copper_mining_2d.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘copper_mining_2d.Rmd’

--- re-building ‘ordinary_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ordinary_kriging.Rmd’

--- re-building ‘simple_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘simple_kriging.Rmd’

--- re-building ‘universal_kriging.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘universal_kriging.Rmd’

SUMMARY: processing the following file failed:
  ‘copper_mining_2d.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘kstIO.Rnw’ using Sweave
Loading required package: pks
Loading required package: sets
Loading required package: MASS
Loading required package: stringr

Attaching package: ‘stringr’

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

    %>%

Loading required package: relations

Error: processing vignette 'kstIO.Rnw' failed with diagnostics:
 chunk 1 
Error in library("kst") : there is no package called ‘kst’

--- failed re-building ‘kstIO.Rnw’

SUMMARY: processing the following file failed:
  ‘kstIO.Rnw’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘Rgraphviz’
Error(s) in re-building vignettes:
--- re-building ‘kst.Rnw’ using Sweave
Loading required package: proxy

Attaching package: ‘proxy’

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

    as.dist, dist

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

    as.matrix

Loading required package: relations
Loading required package: sets
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Loading required namespace: Rgraphviz
Failed with error:  ‘there is no package called ‘Rgraphviz’’
Error: processing vignette 'kst.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'kst.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file ./kst-012.pdf): PDF inclusion: required page does
 not exist <0>
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘kst.Rnw’

SUMMARY: processing the following file failed:
  ‘kst.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.3Mb
installed size is  8.4Mb
  sub-directories of 1Mb or more:
    data   8.2Mb
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/3.6/LambertW.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LANDD.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   2.9Mb
installed size is 144.2Mb
  sub-directories of 1Mb or more:
    libs  142.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘Intro_to_lavaanPlot.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Intro_to_lavaanPlot.Rmd’

SUMMARY: processing the following file failed:
  ‘Intro_to_lavaanPlot.Rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking: 'Rgraphviz', 'graph'
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/3.6/lba.Rcheck/00install.out’ for details.
Found the following significant warnings:
  ./lda_svi.h:1:9: warning: '_lda_svi_guard' is used as a header guard here, followed by #define of a different macro [-Wheader-guard]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/lda.svi.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Learning-leaflet.Rmd’ using rmarkdown
Warning 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 49-69 (Learning-leaflet.Rmd) 
Error: processing vignette 'Learning-leaflet.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Learning-leaflet.Rmd’

--- re-building ‘generic-demo.Rmd’ using rmarkdown
Warning 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 22-46 (generic-demo.Rmd) 
Error: processing vignette 'generic-demo.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘generic-demo.Rmd’

--- re-building ‘leaflethex.Rmd’ using rmarkdown
Warning 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 41-48 (leaflethex.Rmd) 
Error: processing vignette 'leaflethex.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘leaflethex.Rmd’

SUMMARY: processing the following files failed:
  ‘Learning-leaflet.Rmd’ ‘generic-demo.Rmd’ ‘leaflethex.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/leapp.Rcheck/00install.out’ for details.
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  7.7Mb
  sub-directories of 1Mb or more:
    libs   4.7Mb
No protocol specified
Namespace in Imports field not imported from: ‘Rcpp’
  All declared Imports should be used.
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(s) in re-building vignettes:
  ...
--- re-building ‘Understanding_lime.Rmd’ using rmarkdown
Warning 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 262-263 (Understanding_lime.Rmd) 
Error: processing vignette 'Understanding_lime.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Understanding_lime.Rmd’

SUMMARY: processing the following file failed:
  ‘Understanding_lime.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘linkspotterVignette.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘linkspotterVignette.Rmd’

SUMMARY: processing the following file failed:
  ‘linkspotterVignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   9.1Mb
installed size is 28.2Mb
  sub-directories of 1Mb or more:
    R          1.4Mb
    doc        2.4Mb
    libs      21.8Mb
    testdata   1.6Mb
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/3.6/LMERConvenienceFunctions.Rcheck/00install.out’ for details.
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(s) in re-building vignettes:
  ...
--- re-building ‘localsolver.Rmd’ using knitr
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
--- failed re-building ‘localsolver.Rmd’

SUMMARY: processing the following file failed:
  ‘localsolver.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 19.2Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
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/3.6/longitudinalData.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RDRToolbox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/loon.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [10s/24s]
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 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#29) 
  2. Failure: run.cache base.dir in folder that does not have access (@test-run.cache.R#40) 
  
  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/3.6/LOST.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    extdata   4.5Mb
Namespace in Imports field not imported from: ‘ggpubr’
  All declared Imports should be used.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/LSAfun.Rcheck/00install.out’ for details.
installed size is 51.8Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs  49.3Mb
Running examples in ‘LTRCtrees-Ex.R’ failed
The error most likely occurred in:

> ### Name: ICtree
> ### Title: Fit a survival tree for interval-censored survival data
> ### Aliases: ICtree
> 
> ### ** Examples
> 
> library(interval)
Error in library(interval) : there is no package called ‘interval’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LTRCtrees.Rmd’ using rmarkdown
Warning 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 min(diff(sort(ux))) :
  no non-missing arguments to min; returning Inf
Quitting from lines 199-207 (LTRCtrees.Rmd) 
Error: processing vignette 'LTRCtrees.Rmd' failed with diagnostics:
there is no package called 'interval'
--- failed re-building ‘LTRCtrees.Rmd’

SUMMARY: processing the following file failed:
  ‘LTRCtrees.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘LUCIDus-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 62-63 (LUCIDus-vignette.Rmd) 
Error: processing vignette 'LUCIDus-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘LUCIDus-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘LUCIDus-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.6Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.1Mb
    libs   1.7Mb
installed size is 28.7Mb
  sub-directories of 1Mb or more:
    libs  28.4Mb
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/3.6/Maeswrap.Rcheck/00install.out’ for details.
Running ‘testthat.R’ [5s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 12 ]
  1. Error: interactive_blur (@test_interactive_blur.R#6) 
  2. Error: interactive_canny (@test_interactive_canny.R#5) 
  3. Error: interactive_charcoal (@test_interactive_charcoal.R#6) 
  4. Error: interactive_composite (@test_interactive_composite.R#5) 
  5. Error: interactive_despeckle (@test_interactive_despeckle.R#6) 
  6. Error: interactive_emboss (@test_interactive_emboss.R#6) 
  7. Error: interactive_implode (@test_interactive_implode.R#6) 
  8. Error: interactive_modulate (@test_interactive_modulate.R#6) 
  9. Error: interactive_oilpaint (@test_interactive_oilpaint.R#6) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
installed size is 80.1Mb
  sub-directories of 1Mb or more:
    doc    6.7Mb
    libs  72.7Mb
Packages required but not available: 'GO.db', 'lumi', 'WGCNA'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 20.9Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs  19.2Mb
Error(s) in re-building vignettes:
--- re-building ‘manhattanly.Rmd’ using rmarkdown
Warning 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

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]="webshotd4a14dcd902a.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd4a14dcd902a.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
--- failed re-building ‘manhattanly.Rmd’

SUMMARY: processing the following file failed:
  ‘manhattanly.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘manipulateWidgets.Rmd’ using rmarkdown
Warning 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]="webshot26c62068963e.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot26c62068963e.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
--- failed re-building ‘manipulateWidgets.Rmd’

SUMMARY: processing the following file failed:
  ‘manipulateWidgets.Rmd’

Error: Vignette re-building 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/3.6/maotai.Rcheck/00install.out’ for details.
installed size is 20.0Mb
  sub-directories of 1Mb or more:
    doc           1.2Mb
    htmlwidgets   1.4Mb
    libs         16.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
installed size is 12.9Mb
  sub-directories of 1Mb or more:
    java   3.3Mb
    libs   8.3Mb
Package suggested but not available for checking: ‘ASGSCA’
Package which this enhances but not available for checking: ‘graph’
Package unavailable to check Rd xrefs: ‘graph’
Package suggested but not available for checking: ‘kangar00’
Package unavailable to check Rd xrefs: ‘kangar00’
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/3.6/mcca.Rcheck/00install.out’ for details.
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   8.3Mb
Errors in running code in vignettes:
when running code in ‘mcemGLM-vignette.Rnw’
  ...
         6      :  6   6      :  6   Max.   :1.000  
         (Other):324   (Other):324                  

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

Execution halted

... incomplete output.  Crash?
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc   3.0Mb
installed size is 29.3Mb
  sub-directories of 1Mb or more:
    libs  28.3Mb
Running examples in ‘mcStats-Ex.R’ failed
The error most likely occurred in:

> ### Name: showXtremeEventsDis
> ### Title: Show Extreme Events from a Discrete Distribution
> ### Aliases: showXtremeEventsDis
> 
> ### ** Examples
> 
> showXtremeEventsDis("Prop. Test", 3, 5, 0:10, probFun = dbinom, size = 10, prob = 0.5)
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()
> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  5.821 0.142 5.995 0 0 
> grDevices::dev.off()
Error in grDevices::dev.off() : failed to load sRGB colorspace file
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   5.3Mb
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/3.6/MDSMap.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/3.6/mdsOpt.Rcheck/00install.out’ for details.
installed size is 21.2Mb
  sub-directories of 1Mb or more:
    libs  19.6Mb
Packages suggested but not available for checking:
  'TxDb.Hsapiens.UCSC.hg19.knownGene', 'org.Hs.eg.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Mega2R.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   3.2Mb
installed size is  7.7Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    libs   4.6Mb
installed size is 76.9Mb
  sub-directories of 1Mb or more:
    libs  76.5Mb
Packages suggested but not available for checking: 'clpAPI', 'ctc'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/metaboGSE.Rcheck/00install.out’ for details.
No protocol specified

(R:50774): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50780): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50786): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:50792): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50816): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50840): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:50846): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50852): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50858): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:50870): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘MetaIntegrator.Rmd’ using rmarkdown
Warning 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'
--- failed re-building ‘MetaIntegrator.Rmd’

--- re-building ‘MetaIntegratorRealExample.Rmd’ using rmarkdown_notangle
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘MetaIntegratorRealExample.Rmd’

SUMMARY: processing the following file failed:
  ‘MetaIntegrator.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetamapsDB.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'org.Hs.eg.db', 'annaffy', 'hgu133plus2.db', 'hgu133a.db',
  'hgu95av2.db'
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MetaPath.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'GEOquery', 'affy', 'hgu133plus2.db', 'doSMP', 'impute'
Packages suggested but not available for checking:
  'HTSFilter', 'DESeq', 'DESeq2'
Errors in running code in vignettes:
when running code in ‘metaRNASeq.Rnw’
  ...

> options(width = 60)

> library(metaRNASeq)

> library(DESeq2)

  When sourcing ‘metaRNASeq.R’:
Error: there is no package called ‘DESeq2’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘metaRNASeq.Rnw’ using Sweave

Error: processing vignette 'metaRNASeq.Rnw' failed with diagnostics:
 chunk 2 (label = loadparameters) 
Error in library(DESeq2) : there is no package called ‘DESeq2’

--- failed re-building ‘metaRNASeq.Rnw’

SUMMARY: processing the following file failed:
  ‘metaRNASeq.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    libs  58.5Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.1Mb
installed size is  7.0Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    help   2.0Mb
    libs   2.4Mb
installed size is 21.8Mb
  sub-directories of 1Mb or more:
    R      1.2Mb
    doc    1.1Mb
    libs  17.3Mb
    misc   1.1Mb
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  16.9Mb
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/3.6/MFHD.Rcheck/00install.out’ for details.
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  21.0Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘mgwrsar-basic_examples.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘mgwrsar-basic_examples.Rmd’

SUMMARY: processing the following file failed:
  ‘mgwrsar-basic_examples.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘structSSI’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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’ [20s/46s]
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(s) in re-building vignettes:
--- re-building ‘paper.Rnw’ using knitr
Quitting from lines 341-342 (paper.Rnw) 
Error: processing vignette 'paper.Rnw' failed with diagnostics:
subscript out of bounds
--- failed re-building ‘paper.Rnw’

--- re-building ‘tolatex-examples.Rnw’ using knitr
Warning in wilcox.test.default(x = c(-2.17390550005803e-11, -2.17097451127302e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(2.13309370167281e-11, 2.12594386539422e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.99236183107132e-11, 1.97388771994156e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(1.00897068477934e-12, 1.02406971791424e-12,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(8.95727936267576e-13, 8.4909856923332e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.80548975348938e-13, 8.81072992342524e-13,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(5.90887339058099e-11, 6.09077233093558e-11,  :
  cannot compute exact p-value with ties
Warning in wilcox.test.default(x = c(9.97119053991469e-15, 9.92695509127728e-15,  :
  cannot compute exact p-value with ties
--- finished re-building ‘tolatex-examples.Rnw’

SUMMARY: processing the following file failed:
  ‘paper.Rnw’

Error: Vignette re-building failed.
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’
Error(s) in re-building vignettes:
--- re-building ‘milr-intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Use the user-defined lambda vector.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 3.6867.
The penalty term is selected automatically with 50 candidates.
Using the criterion BIC to choose optimized penalty.
The chosen penalty throuth BIC is 4.9895.
The penalty term is selected automatically with 50 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 2.8390.
trying URL 'http://www.cs.columbia.edu/~andrews/mil/data/MIL-Data-2002-Musk-Corel-Trec9.tgz'
Content type 'application/x-gzip' length 6249673 bytes (6.0 MB)
==================================================
downloaded 6.0 MB

Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Warning: 'switch' is deprecated.
Use 'strip.position' instead.
See help("Deprecated")
The penalty term is selected automatically with 100 candidates.
Using the criterion deviance to choose optimized penalty.
The chosen penalty throuth deviance is 3.2909.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.
Use the user-defined lambda vector.

Execution halted
installed size is 22.4Mb
  sub-directories of 1Mb or more:
    libs  22.3Mb
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.9Mb
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/3.6/missDeaths.Rcheck/00install.out’ for details.
installed size is 25.5Mb
  sub-directories of 1Mb or more:
    libs  23.3Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mixKernel.Rcheck/00install.out’ for details.
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
Package suggested but not available for checking: ‘IlluminaHumanMethylation450kmanifest’
Error(s) in re-building vignettes:
  ...
--- re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘comparison_mlr3pipelines_mlr_sklearn.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Warning in png::readPNG(path, native = TRUE, info = TRUE) :
  libpng warning: iCCP: CRC error
Quitting from lines 172-173 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 34.6Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
installed size is 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.6Mb
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/3.6/MMDai.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ALL’
Running examples in ‘MMDvariance-Ex.R’ failed
The error most likely occurred in:

> ### Name: gsMMD.v
> ### Title: Gene selection based on variances by using a mixture of marginal
> ###   distributions
> ### Aliases: gsMMD.v
> ### Keywords: classif
> 
> ### ** Examples
> 
>       t1 = proc.time()
>       library(ALL)
Error in library(ALL) : there is no package called ‘ALL’
Execution halted
Package required but not available: ‘doMPI’

See section ‘The DESCRIPTION file’ 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.
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/3.6/molaR.Rcheck/00install.out’ for details.
installed size is  7.2Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    doc    1.8Mb
    libs   3.3Mb
Packages required but not available: 'org.Hs.eg.db', 'clusterProfiler'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   2.0Mb
    libs   6.2Mb
Error(s) in re-building vignettes:
--- re-building ‘tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 342-344 (tutorial.Rmd) 
Error: processing vignette 'tutorial.Rmd' failed with diagnostics:
The model needs too many iterations to provide reliable parameter estimates !
--- failed re-building ‘tutorial.Rmd’

--- re-building ‘modelling.Snw’ using Sweave
--- finished re-building ‘modelling.Snw’

SUMMARY: processing the following file failed:
  ‘tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
installed size is 16.1Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs  14.0Mb
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.
Package unavailable to check Rd xrefs: ‘Biostrings’
Error(s) in re-building vignettes:
  ...
--- re-building ‘msaR.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘msaR.Rmd’

SUMMARY: processing the following file failed:
  ‘msaR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 42.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.0Mb
    libs  39.9Mb
installed size is 45.9Mb
  sub-directories of 1Mb or more:
    libs  45.4Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘msir.Rmd’ using rmarkdown
Warning 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]="webshot127825d88bea8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot127825d88bea8.png': No such file or directory
Quitting from lines 102-104 (msir.Rmd) 
Error: processing vignette 'msir.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘msir.Rmd’

SUMMARY: processing the following file failed:
  ‘msir.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/MSIseq.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/3.6/MSQC.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    help   1.0Mb
    libs  16.2Mb
Running examples in ‘mssqlR-Ex.R’ failed
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/3.6/mtk.Rcheck/00install.out’ for details.
Running ‘test-all.R’ [30s/31s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Backtrace:
   1. rmarkdown::render(tf, quiet = TRUE)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  OGR: Unsupported geometry type
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 961 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Error: read/write functions work inside RMarkdown (@test_mudata.io.R#554) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required but not available:
  'org.Hs.eg.db', 'org.Mm.eg.db', 'org.Ce.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 83.0Mb
  sub-directories of 1Mb or more:
    libs  82.7Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
Package unavailable to check Rd xrefs: ‘ComplexHeatmap’
Running examples in ‘multistateutils-Ex.R’ failed
The error most likely occurred in:

> ### Name: cohort_simulation
> ### Title: Runs a cohort discrete event simulation
> ### Aliases: cohort_simulation
> 
> ### ** Examples
> 
> library(multistateutils)
> library(mstate)
Loading required package: survival
> library(flexsurv)
> 
> # Convert data to long
> data(ebmt3)
> tmat <- trans.illdeath()
> long <- msprep(time=c(NA, 'prtime', 'rfstime'),
+                status=c(NA, 'prstat', 'rfsstat'),
+                data=ebmt3,
+                trans=tmat,
+                keep=c('age', 'dissub'))
> 
> # Fit parametric models
> models <- lapply(1:3, function(i) {
+     flexsurvreg(Surv(time, status) ~ age + dissub, data=long, dist='weibull')
+ })
> 
> sim <- cohort_simulation(models, ebmt3, tmat)

 *** caught illegal operation ***
address 0x10be47232, cause 'illegal opcode'

Traceback:
 1: desCpp(transitions, trans_mat, newdata_mat, start_times, start_states -     1, tcovs)
 2: data.table::as.data.table(desCpp(transitions, trans_mat, newdata_mat,     start_times, start_states - 1, tcovs))
 3: run_sim(transition_list, attr_mat, trans_mat, tcovs, start_times,     start_states)
 4: state_occupancy(models, trans_mat, newdata, tcovs, start_time,     start_state, ci, M, agelimit, agecol, agescale)
 5: cohort_simulation(models, ebmt3, tmat)
An irrecoverable exception occurred. R is aborting now ...
Running ‘testthat.R’ [4s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  32: withOneRestart(expr, restarts[[1L]])
  33: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  34: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  35: FUN(X[[i]], ...)
  36: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  37: force(code)
  38: doWithOneRestart(return(expr), restart)
  39: withOneRestart(expr, restarts[[1L]])
  40: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  41: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  42: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  43: 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)
  44: 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)
  45: test_check("multistateutils")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 42.1Mb
  sub-directories of 1Mb or more:
    libs  42.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/mvgraphnorm.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/3.6/mvmesh.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette_mvord2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘vignette_mvord2.Rmd’

--- re-building ‘vignette_mvord.Rnw’ using Sweave
Loading required package: minqa
Loading required package: BB
Loading required package: ucminf
Loading required package: dfoptim
Error: processing vignette 'vignette_mvord.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'vignette_mvord.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building 'vignette_mvord.Rnw'

SUMMARY: processing the following file failed:
  ‘vignette_mvord.Rnw’

Error: Vignette re-building failed.
Execution halted
installed size is  9.2Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
Running ‘testthat.R’ [2s/3s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(namer)
  > 
  > test_check("namer")
  ── 1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22)  ───────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  1: rmarkdown::render(temp_file_path) at testthat/test-unname_all_chunks.R:22
  2: pandoc_available(required_pandoc, error = TRUE)
  3: stop(paste(msg, collapse = " "), call. = FALSE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 1
  1. Error: unname_all_chunks works (@test-unname_all_chunks.R#22) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.5Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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/3.6/nat.nblast.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/3.6/nat.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nat.templatebrains.Rcheck/00install.out’ for details.
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(s) in re-building vignettes:
  ...
--- re-building ‘test-vignette.ipynbmeta’ using nbconvert
Error: processing vignette 'test-vignette.ipynbmeta' failed with diagnostics:
Either IPython 3+ or Jupyter has to be installed, but neither could be called.
--- failed re-building ‘test-vignette.ipynbmeta’

SUMMARY: processing the following file failed:
  ‘test-vignette.ipynbmeta’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘sSeq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    data   1.5Mb
    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/3.6/NeatMap.Rcheck/00install.out’ for details.
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.
Package required but not available: ‘ConsensusClusterPlus’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    doc    2.3Mb
    libs   5.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘netgsa.Rmd’ using rmarkdown
Warning 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 86-89 (netgsa.Rmd) 
Error: processing vignette 'netgsa.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘netgsa.Rmd’

SUMMARY: processing the following file failed:
  ‘netgsa.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs   5.4Mb
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/3.6/NetworkDistance.Rcheck/00install.out’ for details.
prepare_Rd: RGL: unable to open X11 display
prepare_Rd: 'rgl_init' failed, running with rgl.useNULL = TRUE
Packages suggested but not available for checking:
  'limma', 'DESeq2', 'edgeR', 'org.Hs.eg.db'
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/3.6/neuroim.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    data   7.6Mb
Error(s) in re-building vignettes:
--- re-building ‘NFP.Rmd’ using rmarkdown
Warning 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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Loading required package: graphite
Quitting from lines 135-143 (NFP.Rmd) 
Error: processing vignette 'NFP.Rmd' failed with diagnostics:
error creating directory: /Users/urbanek/Library/Caches/graphite-bioc/12
--- failed re-building ‘NFP.Rmd’

SUMMARY: processing the following file failed:
  ‘NFP.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 35.2Mb
  sub-directories of 1Mb or more:
    CppCode        1.2Mb
    R              5.8Mb
    classic-bugs   1.5Mb
    include        5.5Mb
    libs          19.0Mb
    tests          1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/NIPTeR.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nlcv.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘geocode.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘geocode.Rmd’

SUMMARY: processing the following file failed:
  ‘geocode.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    libs   6.4Mb
installed size is 16.9Mb
  sub-directories of 1Mb or more:
    libs  15.2Mb
Found the following significant warnings:
  clang-7: warning: treating 'c' input as 'c++' when in C++ mode, this behavior is deprecated [-Wdeprecated]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nloptr.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'doMPI', 'Biobase'
Error loading dataset 'esGolub':
   Error in .requirePackage(package) : 
    unable to find required package 'Biobase'
  
  The dataset(s) may use package(s) not declared in the DESCRIPTION file.
Error(s) in re-building vignettes:
  ...
--- re-building ‘NMF-vignette.Rnw’ using knitr
Quitting from lines 385-398 (NMF-vignette.Rnw) 
Error: processing vignette 'NMF-vignette.Rnw' failed with diagnostics:
unable to find required package 'Biobase'
--- failed re-building ‘NMF-vignette.Rnw’

--- re-building ‘heatmaps.Rnw’ using knitr
Converted 2 of 2 package citations to BibTeX
Writing 4 Bibtex entries ... OK
Results written to file 'Rpackages.bib'
--- finished re-building ‘heatmaps.Rnw’

SUMMARY: processing the following file failed:
  ‘NMF-vignette.Rnw’

Error: Vignette re-building 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/3.6/NNS.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/nonlinearTseries.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
Running examples in ‘noteMD-Ex.R’ failed
The error most likely occurred in:

> ### Name: note_in_html
> ### Title: Print text input in html
> ### Aliases: note_in_html
> 
> ### ** Examples
> 
> note_in_html("Please write note using **Markdown** syntax! ")
sh: +RTS: command not found
Warning in system(command) : error in running command
Error: pandoc document conversion failed with error 127
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/3.6/NPCirc.Rcheck/00install.out’ for details.
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Package suggested but not available for checking: ‘PMA’
installed size is 24.2Mb
  sub-directories of 1Mb or more:
    doc    7.4Mb
    libs  16.4Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    3.2Mb
    libs   2.0Mb
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.
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/3.6/OceanView.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    R      2.3Mb
    doc    2.6Mb
    help   2.6Mb
    libs   3.0Mb
installed size is 82.8Mb
  sub-directories of 1Mb or more:
    libs  82.3Mb
Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ── 2. Failure: OLC encoding throws an error with odd-numbered requested lengths 
  `x` threw an error with unexpected message.
  Expected match: "The length value"
  Actual message: "c++ exception (unknown reason)"
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 34 SKIPPED: 1 FAILED: 2
  1. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#20) 
  2. Failure: OLC encoding throws an error with odd-numbered requested lengths below 8 (@test_encoding.R#21) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  34.7Mb
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.
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/3.6/onemap.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘ontologyPlot’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/OpenCL.Rcheck/00install.out’ for details.
installed size is 74.7Mb
  sub-directories of 1Mb or more:
    libs   64.9Mb
    share   9.7Mb
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs   5.5Mb
installed size is 187.2Mb
  sub-directories of 1Mb or more:
    R         2.5Mb
    libs    177.1Mb
    models    4.6Mb
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/3.6/OpenRepGrid.Rcheck/00install.out’ for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   3.1Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Packages suggested but not available for checking:
  'gurobi', 'ggtree', 'Rsymphony', 'lpsymphony'
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
Package unavailable to check Rd xrefs: ‘ggtree’
Packages suggested but not available for checking:
  'Biobase', 'annotate', 'GO.db', 'org.At.tair.db'
Running ‘bdstest.R’ [2s/4s]
  Running ‘hobbs.R’ [5s/14s]
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/3.6/optiSel.Rcheck/00install.out’ for details.
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    extdata   1.8Mb
    libs      2.7Mb
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/3.6/optiSolve.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘optparse.Rrst’ using knitr
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
--- failed re-building ‘optparse.Rrst’

SUMMARY: processing the following file failed:
  ‘optparse.Rrst’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘ROracle’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    libs   7.6Mb
Packages suggested but not available for checking: 'IsoGene', 'Biobase'
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.
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/3.6/orthoDr.Rcheck/00install.out’ for details.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    3.6Mb
    libs   5.7Mb
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc    3.7Mb
    libs   1.9Mb
Error(s) in re-building vignettes:
--- re-building ‘Rcpp_API.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Rcpp_API.Rmd’

--- re-building ‘customisation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘customisation.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘introduction.Rmd’

--- re-building ‘overview.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
installed size is 10.6Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘graph_packing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘graph_packing.Rmd’

--- re-building ‘intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘intro.Rmd’

--- re-building ‘progressive_packing.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘progressive_packing.Rmd’

SUMMARY: processing the following file failed:
  ‘progressive_packing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PACVr.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/3.6/pals.Rcheck/00install.out’ for details.
Package required but not available: ‘GO.db’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘evals.Rmd’ using rmarkdown
Warning 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 13-19 (evals.Rmd) 
Error: processing vignette 'evals.Rmd' failed with diagnostics:
package or namespace load failed for 'futile.logger' in loadNamespace(j <- i[[1L]], c(lib.loc, .libPaths()), versionCheck = vI[[j]]):
 there is no package called 'formatR'
--- failed re-building ‘evals.Rmd’

--- re-building ‘knitr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘knitr.Rmd’

--- re-building ‘pander.Rmd’ using rmarkdown
Warning 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

--- finished re-building ‘pander.Rmd’

--- re-building ‘pandoc_table.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘pandoc_table.Rmd’

SUMMARY: processing the following file failed:
  ‘evals.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘pandocfilters.Rnw’ using knitr
Quitting from lines 68-69 (pandocfilters.Rnw) 
Error: processing vignette 'pandocfilters.Rnw' failed with diagnostics:
error in running command
--- failed re-building ‘pandocfilters.Rnw’

SUMMARY: processing the following file failed:
  ‘pandocfilters.Rnw’

Error: Vignette re-building failed.
Execution halted
Running examples in ‘ParallelPC-Ex.R’ failed
The error most likely occurred in:

> ### Name: IDA_parallel
> ### Title: Estimate Total Causal Effects using the IDA_parallel Algorithm
> ### Aliases: IDA_parallel
> 
> ### ** Examples
> 
> ##########################################
> ## Using IDA_parallel without mem.efficeient
> ##########################################
> library(bnlearn)

Attaching package: ‘bnlearn’

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

    sigma

> library(pcalg)
Error in library(pcalg) : there is no package called ‘pcalg’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction-to-parcoords-.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 27-30 (introduction-to-parcoords-.Rmd) 
Error: processing vignette 'introduction-to-parcoords-.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction-to-parcoords-.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction-to-parcoords-.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘bes-2015.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘bes-2015.Rmd’

--- re-building ‘bes-2017.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘bes-2017.Rmd’

--- re-building ‘census-11.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘census-11.Rmd’

--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Linking to GEOS 3.6.1, GDAL 2.1.3, PROJ 4.9.3

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Downloading constituency data
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotd60a2e848d62.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotd60a2e848d62.png': No such file or directory
Quitting from lines 65-110 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
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.
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/3.6/patternize.Rcheck/00install.out’ for details.
Packages required but not available: 'jetset', 'Mfuzz', 'WGCNA'

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/3.6/pbdMPI.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdPROF.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pbdZMQ.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/3.6/pca3d.Rcheck/00install.out’ for details.
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc       1.9Mb
    extdata   2.7Mb
    libs      2.1Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pcaL1.Rcheck/00install.out’ for details.
installed size is 12.1Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   6.9Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
installed size is 99.2Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs  96.2Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PCGSE.Rcheck/00install.out’ for details.
installed size is 35.3Mb
  sub-directories of 1Mb or more:
    libs  34.2Mb
Package suggested but not available for checking: ‘ggtree’
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/3.6/PCRedux.Rcheck/00install.out’ for details.
installed size is 18.5Mb
  sub-directories of 1Mb or more:
    libs    6.5Mb
    share  11.9Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package suggested but not available for checking: ‘globaltest’
Found the following significant warnings:
  Warning: package ‘biomaRt’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PepPrep.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/permGPU.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘BiocParallel’
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/3.6/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.
Package suggested but not available for checking: ‘RankProd’
Package unavailable to check Rd xrefs: ‘RankProd’
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  35.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘phybreak_intro.Rmd’ using rmarkdown
Warning 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
Error(s) in re-building vignettes:
--- re-building ‘Advanced_Usage.Rmd’ using rmarkdown
Warning 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]="webshotc4dc454c7107.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotc4dc454c7107.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
--- failed re-building ‘Advanced_Usage.Rmd’

--- re-building ‘Basic_Use.Rmd’ using rmarkdown
Warning 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 30-32 (Basic_Use.Rmd) 
Error: processing vignette 'Basic_Use.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Basic_Use.Rmd’

SUMMARY: processing the following files failed:
  ‘Advanced_Usage.Rmd’ ‘Basic_Use.Rmd’

Error: Vignette re-building 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/3.6/phylocurve.Rcheck/00install.out’ for details.
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    libs   9.3Mb
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    doc    2.0Mb
    libs   9.3Mb
Running examples in ‘pingr-Ex.R’ failed
The error most likely occurred in:

> ### Name: my_ip
> ### Title: Query the computer's public IP address
> ### Aliases: my_ip
> 
> ### ** Examples
> 
> my_ip()
Error in nsl("myip.opendns.com", server = "208.67.222.222", type = 1L) : 
  DNS query failed (system error 61, Connection refused) @dns.c:324 (r_nsl)
Calls: my_ip -> my_ip_dns -> nsl
Execution halted
Running ‘testthat.R’ [2s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 44 | SKIPPED: 0 | WARNINGS: 19 | FAILED: 36 ]
  1. Failure: We can download files to a local dir without MD5 check. (@test-filecache.R#20) 
  2. Failure: We can download files to a local dir without MD5 check. (@test-filecache.R#21) 
  3. Failure: We can download files to a local dir without MD5 check. (@test-filecache.R#22) 
  4. Failure: We can download files to a local dir without MD5 check. (@test-filecache.R#23) 
  5. Failure: We can download files to a local dir without MD5 check. (@test-filecache.R#24) 
  6. Failure: We can erase the file cache and list all files in the cache (@test-filecache.R#57) 
  7. Failure: We can erase the file cache and list all files in the cache (@test-filecache.R#59) 
  8. Failure: We can erase the file cache and list all files in the cache (@test-filecache.R#60) 
  9. Failure: We can erase the file cache and list all files in the cache (@test-filecache.R#61) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: ‘rggobi’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 25.4Mb
  sub-directories of 1Mb or more:
    libs  25.3Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PlasmaMutationDetector.Rcheck/00install.out’ for details.
Package unavailable to check Rd xrefs: ‘S4Vectors’
No protocol specified

(R:76720): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:76728): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:76736): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:76744): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:76770): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:76798): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:76806): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:76814): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:76822): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
No protocol specified

(R:76836): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   7.6Mb
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/3.6/plot3Drgl.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘using_plotdap.Rmd’ using rmarkdown
Warning 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 138-146 (using_plotdap.Rmd) 
Error: processing vignette 'using_plotdap.Rmd' failed with diagnostics:
Failed to open file /Users/urbanek/Library/Caches/R/rerddap/d3691d4726dcf37b41ff22352dc3ac7e.nc.
--- failed re-building ‘using_plotdap.Rmd’

SUMMARY: processing the following file failed:
  ‘using_plotdap.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    htmlwidgets   3.6Mb
Package suggested but not available for checking: ‘mixOmics’
Running examples in ‘PLSbiplot1-Ex.R’ failed
The error most likely occurred in:

> ### Name: Mag.Bmat.plot
> ### Title: Magnitude of the Partial Least Squares Regression (PLSR)
> ###   coefficients matrix
> ### Aliases: Mag.Bmat.plot
> 
> ### ** Examples
> 
> if(require(pls))
+ data(oliveoil, package="pls")
Loading required package: pls

Attaching package: ‘pls’

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

    loadings

> X = as.matrix(oliveoil$chemical, ncol=5)
> dimnames(X) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Acidity","Peroxide","K232","K270","DK")))
> Y = as.matrix(oliveoil$sensory, ncol=6)
> dimnames(Y) = list(paste(c("G1","G2","G3","G4","G5","I1","I2","I3","I4","I5",
+ "S1","S2","S3","S4","S5","S6")),
+ paste(c("Yellow","Green","Brown","Glossy","Transp","Syrup")))
> Mag.Bmat.plot(X, Y, algorithm=mod.SIMPLS, A=2)
> 
> #nutrimouse data
> if(require(mixOmics))
+ data(nutrimouse, package="mixOmics")
Loading required package: mixOmics
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘mixOmics’
> X1 = as.matrix(nutrimouse$lipid, ncol=21)
Error in as.matrix(nutrimouse$lipid, ncol = 21) : 
  object 'nutrimouse' not found
Execution halted
Packages required but not available: 'pbdMPI', 'pbdBASE', 'pbdDMAT'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
--- re-building ‘pmc_tutorial.Rmd’ using rmarkdown
Warning 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: subplex

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

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

Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘vignette.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘polynomials.Rmd’ using rmarkdown
Warning 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 'polynomials.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘polynomials.Rmd’

SUMMARY: processing the following file failed:
  ‘polynomials.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘EmpiricalBrownsMethod’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  whopgenome/whoptbi_info.cpp:116:6: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_info.cpp:122:7: warning: reference cannot be bound to dereferenced null pointer in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
  whopgenome/whoptbi_region.cpp:80:13: warning: 'this' pointer cannot be null in well-defined C++ code; comparison may be assumed to always evaluate to false [-Wtautological-undefined-compare]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/PopGenome.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘lfa’
Package suggested but not available for checking: ‘VariantAnnotation’
Package required but not available: ‘Rsymphony’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
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/3.6/PPQplan.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘PPQnote.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘PPQnote.Rmd’

--- re-building ‘PPQplan-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
No protocol specified
Warning in normalizePath(f2) :
  path[1]="webshot83bd39d2f15.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot83bd39d2f15.png': No such file or directory
Quitting from lines 135-136 (PPQplan-vignette.Rmd) 
Error: processing vignette 'PPQplan-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PPQplan-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘PPQplan-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Package suggested but not available for checking: ‘PerfMeas’
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/3.6/predict3d.Rcheck/00install.out’ for details.
No protocol specified
Namespaces in Imports field not imported from:
  ‘TH.data’ ‘moonBook’
  All declared Imports should be used.
Error(s) in re-building vignettes:
  ...
--- re-building ‘predict3d.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: predict3d
No protocol specified
Loading required package: rgl
Quitting from lines 55-58 (predict3d.Rmd) 
Error: processing vignette 'predict3d.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘predict3d.Rmd’

SUMMARY: processing the following file failed:
  ‘predict3d.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 17.1Mb
  sub-directories of 1Mb or more:
    libs  16.7Mb
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/3.6/prim.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'gurobi', 'Rsymphony'
installed size is 11.4Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs   8.2Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘PRISMA.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 39-52 (PRISMA.Rmd) 
Error: processing vignette 'PRISMA.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PRISMA.Rmd’

--- re-building ‘exclusionflowcharts.Rmd’ using rmarkdown
Warning 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 25-31 (exclusionflowcharts.Rmd) 
Error: processing vignette 'exclusionflowcharts.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘exclusionflowcharts.Rmd’

SUMMARY: processing the following files failed:
  ‘PRISMA.Rmd’ ‘exclusionflowcharts.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.5Mb
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc           9.2Mb
    htmlwidgets   2.5Mb
installed size is 15.4Mb
  sub-directories of 1Mb or more:
    extdata   7.4Mb
    libs      6.9Mb
Package suggested but not available for checking: ‘EBImage’
Running examples in ‘proftools-Ex.R’ failed
The error most likely occurred in:

> ### Name: filterProfileData
> ### Title: Filter Profile Data
> ### Aliases: filterProfileData
> ### Keywords: programming utilities
> 
> ### ** Examples
> 
> pd <- readProfileData(system.file("samples", "glmEx.out", package="proftools"))
> plotProfileCallGraph(pd)
Error in loadNamespace(name) : there is no package called ‘graph’
Calls: plotProfileCallGraph ... loadNamespace -> withRestarts -> withOneRestart -> doWithOneRestart
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘proftools.Rnw’ using knitr
Quitting from lines 221-222 (proftools.Rnw) 
Error: processing vignette 'proftools.Rnw' failed with diagnostics:
there is no package called 'graph'
--- failed re-building ‘proftools.Rnw’

SUMMARY: processing the following file failed:
  ‘proftools.Rnw’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'qtbase', 'RGtk2', 'cairoDevice', 'gWidgetsRGtk2'
Running ‘testthat.R’ [73s/74s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
                                                            ^
  21 warnings generated.
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 289 | SKIPPED: 1 | WARNINGS: 1 | FAILED: 8 ]
  1. Error: cross_validation (@test_diagnostics.R#20) 
  2. Error: cross_validation_logistic (@test_diagnostics.R#46) 
  3. Error: cross_validation_extra_regressors (@test_diagnostics.R#66) 
  4. Error: cross_validation_default_value_check (@test_diagnostics.R#81) 
  5. Error: performance_metrics (@test_diagnostics.R#91) 
  6. Error: fit_predict_no_changepoints (@test_prophet.R#28) 
  7. Error: fit_predict_changepoint_not_in_history (@test_prophet.R#42) 
  8. Error: auto_weekly_seasonality (@test_prophet.R#415) 
  
  Error: testthat unit tests failed
  Execution halted
Packages suggested but not available for checking:
  'ALDEx2', 'Biobase', 'limma'
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    libs   2.8Mb
Packages suggested but not available for checking:
  'Biostrings', 'GOSemSim', 'org.Hs.eg.db'
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    libs   3.0Mb
Package suggested but not available for checking: ‘zoo’
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/3.6/ptinpoly.Rcheck/00install.out’ for details.
Package required but not available: ‘tweeDEseq’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Running ‘testthat.R’ [40s/38s]
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) : 88.8 | 88.5 | 3859256 (3859167)
  
  Duration: 0 s
  
  ... MS/MS Peak shape  done
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 119 SKIPPED: 0 WARNINGS: 128 FAILED: 2
  1. Failure: createReport (@test_computeQC.R#46) 
  2. Failure: createReport (@test_computeQC.R#47) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 36.0Mb
  sub-directories of 1Mb or more:
    libs  35.5Mb
Package suggested but not available for checking: ‘TxDb.Hsapiens.UCSC.hg19.knownGene’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/pulseTD.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘Data_Model.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Data_Model.Rmd’

--- re-building ‘Maps_and_Timeseries_Plots.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘Maps_and_Timeseries_Plots.Rmd’

--- re-building ‘NowCast.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NowCast.Rmd’

--- re-building ‘PWFSLSmoke.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 163-164 (PWFSLSmoke.Rmd) 
Error: processing vignette 'PWFSLSmoke.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘PWFSLSmoke.Rmd’

SUMMARY: processing the following file failed:
  ‘PWFSLSmoke.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    gui          1.1Mb
    staticdocs   3.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qMRI.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qpcR.Rcheck/00install.out’ for details.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    libs  15.4Mb
Found the following executable file:
  src/LZ4/LICENSE.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/qtbase.Rcheck/00install.out’ for details.
installed size is 21.7Mb
  sub-directories of 1Mb or more:
    libs  21.0Mb
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/3.6/qtlc.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  7.7Mb
  sub-directories of 1Mb or more:
    libs   7.3Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘wilcox1973.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘wilcox1973.Rmd’

SUMMARY: processing the following file failed:
  ‘wilcox1973.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 14.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   1.3Mb
    libs  11.1Mb
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/3.6/QuantifQuantile.Rcheck/00install.out’ for details.
installed size is  9.1Mb
  sub-directories of 1Mb or more:
    data   4.5Mb
    libs   3.9Mb
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.
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.
Error(s) in re-building vignettes:
  ...
--- re-building ‘R2admb.Rnw’ using knitr
Error: processing vignette 'R2admb.Rnw' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘R2admb.Rnw’

SUMMARY: processing the following file failed:
  ‘R2admb.Rnw’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/R2GUESS.Rcheck/00install.out’ for details.
'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/3.6/R330.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RAbHIT-vignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: ggplot2
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshot11ecc22868ec0.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot11ecc22868ec0.png': No such file or directory
Quitting from lines 285-287 (RAbHIT-vignette.Rmd) 
Error: processing vignette 'RAbHIT-vignette.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘RAbHIT-vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘RAbHIT-vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    data   2.1Mb
    doc    5.9Mb
    libs   1.1Mb
No protocol specified
No protocol specified
Namespaces in Imports field not imported from:
  ‘KernSmooth’ ‘Matrix’ ‘PharmacoGx’ ‘cluster’
  All declared Imports should be used.
No protocol specified
  No protocol specified
  Note: found 26 marked UTF-8 strings
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/3.6/RadOnc.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  5.7Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    libs   9.1Mb
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/3.6/RAINBOWR.Rcheck/00install.out’ for details.
installed size is 31.4Mb
  sub-directories of 1Mb or more:
    libs  30.5Mb
installed size is 11.8Mb
  sub-directories of 1Mb or more:
    api           3.1Mb
    htmlwidgets   7.0Mb
Package unavailable to check Rd xrefs: ‘Heatplus’
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    help   1.2Mb
    libs   4.6Mb
Package unavailable to check Rd xrefs: ‘WGCNA’
Package suggested but not available for checking: ‘BSgenome.Hsapiens.UCSC.hg19’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RAPIDR.Rcheck/00install.out’ for details.
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    data   3.6Mb
    doc    1.4Mb
    libs   9.6Mb
Package suggested but not available for checking: ‘rpanel’
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/3.6/rase.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning 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: 'lubridate'

The following objects are masked from 'package:data.table':

    hour, isoweek, mday, minute, month, quarter, second, wday,
    week, yday, year

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

    date

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 130-141 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    R      2.5Mb
    libs   6.5Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   4.5Mb
Packages suggested but not available for checking:
  'cairoDevice', 'gWidgetsRGtk2', 'playwith', 'rggobi', 'RGtk2',
  'RGtk2Extras'
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rayshader.Rcheck/00install.out’ for details.
installed size is 34.7Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs  31.0Mb
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rblpapi.Rcheck/00install.out’ for details.
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    blp    5.9Mb
    libs   5.2Mb
Package required but not available: ‘h5’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘RCAL-vig.Rnw’ using Sweave
Loading required package: trust

Execution halted
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 12.2Mb
  sub-directories of 1Mb or more:
    libs  11.9Mb
Found the following significant warnings:
  Warning: package ‘AnnotationDbi’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.BiclustGUI.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/3.6/RcmdrPlugin.RiskDemo.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
  Warning: loading Rplot failed
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcmdrPlugin.TeachingDemos.Rcheck/00install.out’ for details.
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/3.6/Rcplex.Rcheck/00install.out’ for details.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    include   5.9Mb
    libs      1.9Mb
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppClassic.Rcheck/00install.out’ for details.
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    lib    3.1Mb
    libs   1.5Mb
installed size is 32.8Mb
  sub-directories of 1Mb or more:
    include   7.6Mb
    libs     24.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMeCab.Rcheck/00install.out’ for details.
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RcppMLPACK.Rcheck/00install.out’ for details.
installed size is 37.3Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib      25.5Mb
    libs      9.9Mb
installed size is  9.6Mb
  sub-directories of 1Mb or more:
    include   6.7Mb
    libs      2.5Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 13.8Mb
  sub-directories of 1Mb or more:
    doc       1.0Mb
    include   6.2Mb
    libs      4.7Mb
installed size is  5.5Mb
  sub-directories of 1Mb or more:
    libs   5.2Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   4.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rcrypt.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rdf_intro.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

Quitting from lines 41-42 (rdf_intro.Rmd) 
Error: processing vignette 'rdf_intro.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rdf_intro.Rmd’

SUMMARY: processing the following file failed:
  ‘rdf_intro.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 13.3Mb
  sub-directories of 1Mb or more:
    libs  11.8Mb
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/3.6/rdist.Rcheck/00install.out’ for details.
Running examples in ‘Rdsm-Ex.R’ failed
The error most likely occurred in:

> ### Name: readsync
> ### Title: Syncing file-backed variables.
> ### Aliases: readsync writesync
> 
> ### ** Examples
> 
> library(parallel)
> c2 <- makeCluster(2)
> mgrinit(c2)
Warning in for (v in val) { :
  closing unused connection 6 (<-localhost:11715)
Warning in for (v in val) { :
  closing unused connection 5 (<-localhost:11715)
[[1]]
[1] 0

[[2]]
[1] 0

> mgrmakevar(c2,"x",1,1,fs=TRUE)
Error in bigmemory::filebacked.big.matrix(nrow = nr, ncol = nc, type = vartype,  : 
  Backing file already exists! Either remove or specify
           different backing file
Calls: mgrmakevar -> <Anonymous>
Execution halted
installed size is 10.4Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs   7.8Mb
Error(s) in re-building vignettes:
--- re-building ‘recexcavAAR-vignette-1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-1.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-1.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-1.Rmd’

--- re-building ‘recexcavAAR-vignette-2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-2.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-2.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-2.Rmd’

--- re-building ‘recexcavAAR-vignette-3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (recexcavAAR-vignette-3.Rmd) 
Error: processing vignette 'recexcavAAR-vignette-3.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.13.1; older versions will not work.
--- failed re-building ‘recexcavAAR-vignette-3.Rmd’

SUMMARY: processing the following files failed:
  ‘recexcavAAR-vignette-1.Rmd’ ‘recexcavAAR-vignette-2.Rmd’
  ‘recexcavAAR-vignette-3.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    doc    3.3Mb
    libs   2.5Mb
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   4.1Mb
installed size is 17.7Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  15.3Mb
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/3.6/red.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    data   1.6Mb
    libs   3.7Mb
Packages suggested but not available for checking: 'interval', 'Icens'
Package unavailable to check Rd xrefs: ‘interval’
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc    8.6Mb
    libs   2.4Mb
Error(s) in re-building vignettes:
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning 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: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 107-117 (getting-started.Rmd) 
Error: processing vignette 'getting-started.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘getting-started.Rmd’

--- re-building ‘means-rotation.Rmd’ using rmarkdown
Warning 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: 'rENA'

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

    show

Loading required package: ggplot2

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Quitting from lines 56-82 (means-rotation.Rmd) 
Error: processing vignette 'means-rotation.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘means-rotation.Rmd’

SUMMARY: processing the following files failed:
  ‘getting-started.Rmd’ ‘means-rotation.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [35s/35s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  	R_LIBS      : <NA>
  	R_LIBS_SITE : ""
  	R_LIBS_USER : "~/Library/R/3.6/library"
  
  > 
  > test_check("renv")
  ── 1. Failure: renv warns when installing an already-loaded package (@test-insta
  `install("bread@0.1.0")` did not produce any warnings.
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 262 | SKIPPED: 42 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: renv warns when installing an already-loaded package (@test-install.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
Running ‘testthat.R’ [2s/5s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ── 2. Error: Testing the introduction presentation (@test-SlideDeck.R#6)  ──────
  Please install either RStudio or Pandoc (https://pandoc.org)
  1: Read()$auto(tfname, quiet = TRUE) at testthat/test-SlideDeck.R:6
  2: get(fileExt, mode = "function")(fileName, ...)
  3: md(mdFile)
  4: knitr::pandoc(fileName, format = "plain")
  5: stop("Please install either RStudio or Pandoc (https://pandoc.org)")
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  OK: 10 SKIPPED: 0 FAILED: 2
  1. Error:  (@test-Evaluate.R#7) 
  2. Error: Testing the introduction presentation (@test-SlideDeck.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    libs   8.4Mb
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    data   3.1Mb
    libs   1.8Mb
Found the following significant warnings:
  regalg.cpp:215:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
  regalg.cpp:454:10: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/resemble.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘rsolr’
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/3.6/restlos.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘log_parsing.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Read 1000 items
`stat_bin()` using `bins = 30`. Pick better value with `binwidth`.
--- finished re-building ‘log_parsing.Rmd’

--- re-building ‘url_parsing.Rmd’ using rmarkdown
Warning 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 'url_parsing.Rmd' failed with diagnostics:
there is no package called 'stringi'
--- failed re-building ‘url_parsing.Rmd’

SUMMARY: processing the following file failed:
  ‘url_parsing.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 33.9Mb
  sub-directories of 1Mb or more:
    libs  32.6Mb
Package suggested but not available for checking: ‘MKmisc’
Running examples in ‘RFLPtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: RFLPtools-package
> ### Title: Tools to analyse RFLP-data
> ### Aliases: RFLPtools-package RFLPtools
> ### Keywords: package multivariate cluster
> 
> ### ** Examples
> 
> data(RFLPdata)
> res <- RFLPdist(RFLPdata)
> plot(hclust(res[[1]]), main = "Euclidean distance")
> 
> par(mfrow = c(1,2))
> plot(hclust(RFLPdist(RFLPdata, nrBands = 3)), cex = 0.7)
> RFLPplot(RFLPdata, nrBands = 3, mar.bottom = 6, cex.axis = 0.8)
> 
> data(RFLPref)
> RFLPrefplot(RFLPdata, RFLPref, nrBands = 6, cex.axis = 0.8)
> 
> 
> library(MKmisc)
Error in library(MKmisc) : there is no package called ‘MKmisc’
Execution halted
Errors in running code in vignettes:
when running code in ‘RFLPtools.Rnw’
  ...
 - attr(*, "Diag")= logi FALSE
 - attr(*, "Upper")= logi FALSE
 - attr(*, "method")= chr "maximum"
 - attr(*, "call")= language dist(x = x, method = "maximum")

> library(MKmisc)

  When sourcing ‘RFLPtools.R’:
Error: there is no package called ‘MKmisc’
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘RFLPtools.Rnw’ using Sweave
Loading required package: RColorBrewer

Error: processing vignette 'RFLPtools.Rnw' failed with diagnostics:
 chunk 5 (label = cor) 
Error in library(MKmisc) : there is no package called ‘MKmisc’

--- failed re-building ‘RFLPtools.Rnw’

SUMMARY: processing the following file failed:
  ‘RFLPtools.Rnw’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
--- re-building ‘rfm-customer-level-data.Rmd’ using rmarkdown
Warning 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 object is masked from 'package:kableExtra':

    group_rows

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
--- failed re-building ‘rfm-customer-level-data.Rmd’

--- re-building ‘rfm-transaction-level-data.Rmd’ using rmarkdown
Warning 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 object is masked from 'package:kableExtra':

    group_rows

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 227-271 (rfm-transaction-level-data.Rmd) 
Error: processing vignette 'rfm-transaction-level-data.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rfm-transaction-level-data.Rmd’

SUMMARY: processing the following files failed:
  ‘rfm-customer-level-data.Rmd’ ‘rfm-transaction-level-data.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 144.9Mb
  sub-directories of 1Mb or more:
    libs      142.0Mb
    pictures    1.3Mb
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   3.5Mb
    libs      1.6Mb
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 21.7Mb
  sub-directories of 1Mb or more:
    libs  20.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rggobi.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rgl.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    doc     3.6Mb
    fonts   1.5Mb
    libs    4.2Mb
No protocol specified
Warning in rgl.init(initValue, onlyNULL) :
  RGL: unable to open X11 display
Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE

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(s) in re-building vignettes:
--- re-building ‘WebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (WebGL.Rmd) 
Error: processing vignette 'WebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘WebGL.Rmd’

--- re-building ‘legacyWebGL.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 17-19 (legacyWebGL.Rmd) 
Error: processing vignette 'legacyWebGL.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘legacyWebGL.Rmd’

--- re-building ‘rgl.Rmd’ using rmarkdown
Warning 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 16-19 (rgl.Rmd) 
Error: processing vignette 'rgl.Rmd' failed with diagnostics:
These vignettes assume pandoc version 1.14; older versions may not work.
--- failed re-building ‘rgl.Rmd’

SUMMARY: processing the following files failed:
  ‘WebGL.Rmd’ ‘legacyWebGL.Rmd’ ‘rgl.Rmd’

Error: Vignette re-building 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/3.6/rglwidget.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rgnuplot.Rcheck/00install.out’ for details.
Packages suggested but not available for checking:
  'graph', 'gWidgetsRGtk2', 'hyperdraw', 'hypergraph', 'playwith',
  'pmg', 'rggobi', 'Rgraphviz', 'SVGAnnotation'
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    R      3.7Mb
    help  11.1Mb
    libs   9.6Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_rhandsontable.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘intro_rhandsontable.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_rhandsontable.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rhpc.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: loading Rplot failed
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RHRV.Rcheck/00install.out’ for details.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
Namespaces in Imports field not imported from:
  ‘httr’ ‘remotes’ ‘rmarkdown’ ‘shiny’
  All declared Imports should be used.
Package unavailable to check Rd xrefs: ‘installr’
Found the following significant warnings:
  WARNING: shared objects/dynamic libraries with hard-coded temporary installation paths
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RInside.Rcheck/00install.out’ for details.
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.
installed size is 13.0Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
installed size is 23.8Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  22.2Mb
Running examples in ‘RISmed-Ex.R’ failed
The error most likely occurred in:

> ### Name: Cited
> ### Title: Number of citations
> ### Aliases: Cited
> 
> ### ** Examples
> 
> res <- EUtilsSummary("myeloma[ti]", mindate = "2002/01/01", maxdate = "2002/02/01", retmax = 5)
> Cited(res)
Warning in readLines(the_url) :
  cannot open URL 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor': HTTP status was '429 Unknown Error'
Error in readLines(the_url) : 
  cannot open the connection to 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?retmode=xml&dbfrom=pubmed&id=11818668&cmd=neighbor'
Calls: Cited -> Cited -> sapply -> lapply -> FUN -> readLines
Execution halted
Running examples in ‘RiverLoad-Ex.R’ failed
The error most likely occurred in:

> ### Name: method4
> ### Title: Load estimation with time-weighted concentration method
> ### Aliases: method4
> ### Keywords: univ
> 
> ### ** Examples
> 
> data("flow.data1", "conc.data1")
> union<-db.union(flow.data1, conc.data1)
> met4<-method4(union, 2)
> met4.month<-method4(union, 2, "month")
Error in x[[jj]][iseq] <- vjj : replacement has length zero
Calls: method4 -> [<- -> [<-.data.frame
Execution halted
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/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.
installed size is 19.1Mb
  sub-directories of 1Mb or more:
    libs  18.9Mb
Packages suggested but not available for checking:
  'Biobase', 'genefilter', 'golubEsets'
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/3.6/Rknots.Rcheck/00install.out’ for details.
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    libs   8.3Mb
installed size is  6.4Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
installed size is 44.4Mb
  sub-directories of 1Mb or more:
    libs  43.8Mb
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/3.6/rLiDAR.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rLindo.Rcheck/00install.out’ for details.
Mallows: no visible global function definition for ‘runif’
Mallows: no visible global function definition for ‘x11’
Mallows: no visible global function definition for ‘plot’
Mallows: no visible global function definition for ‘dev.off’
UpdateLambda: no visible global function definition for ‘uniroot’
Undefined global functions or variables:
  dev.off plot runif uniroot x11
Consider adding
  importFrom("grDevices", "dev.off", "x11")
  importFrom("graphics", "plot")
  importFrom("stats", "runif", "uniroot")
to your NAMESPACE file.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.8Mb
Missing or unexported object: ‘tidyr::one_of’
installed size is  9.0Mb
  sub-directories of 1Mb or more:
    rmd   8.2Mb
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/3.6/RMark.Rcheck/00install.out’ for details.
installed size is 52.2Mb
  sub-directories of 1Mb or more:
    libs  51.6Mb
Running ‘spelling.R’ [0s/0s]
  Running ‘testthat.R’ [1s/2s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  argument is of length zero
  Backtrace:
   1. testthat::expect_identical(...)
   4. rmdfiltr::add_lua_filter(...)
   5. rmdfiltr::add_custom_filter(...)
   6. rmdfiltr::verify_pandoc_version(report = report)
   7. utils::compareVersion("2.0", as.character(rmarkdown::pandoc_version()))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 0 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: Convenience functions (@test_convenience_functions.R#4) 
  2. Error: Vectorization (@test_vectorization.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RmecabKo.Rcheck/00install.out’ for details.
installed size is  8.7Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   5.7Mb
installed size is 41.3Mb
  sub-directories of 1Mb or more:
    libs  40.5Mb
installed size is 29.8Mb
  sub-directories of 1Mb or more:
    doc    1.5Mb
    libs  28.2Mb
Running ‘testthat.R’ [138s/138s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  k: 1, sd      1.730696    1.693051     1.821035
  k: 2, mean:   3.376765    3.352140     3.420286
  k: 2, sd      1.744143    1.716011     1.778174
  Start run 1
  Run 1 DONE 
  $warnLog
  [1] "Crash."
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 371 | SKIPPED: 2 | WARNINGS: 2 | FAILED: 2 ]
  1. Failure: mixtCompLearn works in basic mode + predict (@test.runWrapper.R#74) 
  2. Failure: mixtCompLearn works in basic mode + predict (@test.runWrapper.R#95) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rMouse.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rmpi.Rcheck/00install.out’ for details.
Package required but not available: ‘splineTimeR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is 12.7Mb
  sub-directories of 1Mb or more:
    libs  12.4Mb
installed size is 18.8Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
Packages suggested but not available for checking: 'topGO', 'DESeq'
Packages unavailable to check Rd xrefs: ‘DESeq’, ‘topGO’
installed size is 20.3Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    doxygen   1.5Mb
    libs      3.2Mb
installed size is 97.5Mb
  sub-directories of 1Mb or more:
    extdata   2.0Mb
    libs     95.4Mb
Found the following executable files:
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R1/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R2/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R3/10/fid
  inst/extra/CD_BBI_16P02/CD_BBI_16P02-R8/10/fid
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro.Rmd’ using rmarkdown
Warning 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 188-195 (intro.Rmd) 
Error: processing vignette 'intro.Rmd' failed with diagnostics:
Column `is_oa` is unknown
--- failed re-building ‘intro.Rmd’

SUMMARY: processing the following file failed:
  ‘intro.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘gprege’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Packages suggested but not available for checking:
  'affydata', 'hgu95av2cdf', 'beadarrayExampleData',
  'illuminaHumanv3.db'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RobLoxBioC.Rcheck/00install.out’ for details.
installed size is 16.6Mb
  sub-directories of 1Mb or more:
    libs  16.3Mb
installed size is 26.4Mb
  sub-directories of 1Mb or more:
    libs  26.0Mb
installed size is 33.0Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
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/3.6/RockFab.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/3.6/ROCS.Rcheck/00install.out’ for details.
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.
installed size is 20.1Mb
  sub-directories of 1Mb or more:
    libs  20.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROpenCVLite.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘RobLox’
Package unavailable to check Rd xrefs: ‘RobLox’
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ROracle.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/3.6/rotations.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.1Mb
    data   2.3Mb
    libs   4.9Mb
installed size is  5.7Mb
  sub-directories of 1Mb or more:
    R       2.0Mb
    libs    2.1Mb
    tests   1.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpanel.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/3.6/Rpdb.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rpg.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘seqLogo’
installed size is  6.8Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      4.1Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘NEWS.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘NEWS.Rmd’

--- re-building ‘rpivotTableIntroduction.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘rpivotTableIntroduction.Rmd’

SUMMARY: processing the following file failed:
  ‘rpivotTableIntroduction.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.6Mb
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/3.6/Rpolyhedra.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rpoppler.Rcheck/00install.out’ for details.
installed size is 26.2Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs  24.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rquake.Rcheck/00install.out’ for details.
installed size is 85.6Mb
  sub-directories of 1Mb or more:
    libs  85.0Mb
installed size is 32.3Mb
  sub-directories of 1Mb or more:
    libs  31.6Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/rrd.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘rrtable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: moonBook
Loading required package: ztable
Welcome to package ztable ver 0.2.0
Loading required package: rrtable

Attaching package: 'rrtable'

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

    roundDf

Loading required package: ggplot2
Quitting from lines 68-69 (rrtable.Rmd) 
Error: processing vignette 'rrtable.Rmd' failed with diagnostics:
`render_flextable` needs to be used as a renderer for a knitr/rmarkdown R code chunk (render by rmarkdown)
--- failed re-building ‘rrtable.Rmd’

SUMMARY: processing the following file failed:
  ‘rrtable.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    dependencies  20.2Mb
Note: information on .o files is not available
File ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rserve.Rcheck/Rserve/libs/Rserve.so’:
  Found ‘_exit’, possibly from ‘exit’ (C)
  Found ‘_rand’, possibly from ‘rand’ (C)
  Found ‘_random’, possibly from ‘random’ (C)
  Found ‘_srandom’, possibly from ‘srandom’ (C)
File ‘Rserve/libs/Rserve.so’:
  Found non-API call to R: ‘R_TempDir’

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

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

Depends: includes the non-default packages:
  'biwt', 'cairoDevice', 'fBasics', 'gplots', 'gWidgets',
  'gWidgetsRGtk2', 'minerva', 'parmigene', 'stringr', 'snowfall'
Adding so many packages to the search path is excessive and importing
selectively is preferable.
File ‘rsgcc/libs/rsgcc.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.
installed size is 23.0Mb
  sub-directories of 1Mb or more:
    libs  21.2Mb
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    libs  15.5Mb
installed size is 10.9Mb
  sub-directories of 1Mb or more:
    libs  10.2Mb
installed size is 45.2Mb
  sub-directories of 1Mb or more:
    libs  44.6Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    libs  10.9Mb
installed size is 145.8Mb
  sub-directories of 1Mb or more:
    R       1.5Mb
    doc     1.2Mb
    libs  142.5Mb
installed size is 28.3Mb
  sub-directories of 1Mb or more:
    libs  28.0Mb
installed size is 233.2Mb
  sub-directories of 1Mb or more:
    libs  230.5Mb
installed size is 69.5Mb
  sub-directories of 1Mb or more:
    libs  68.3Mb
installed size is 16.2Mb
  sub-directories of 1Mb or more:
    doc    1.4Mb
    libs  13.2Mb
installed size is 61.3Mb
  sub-directories of 1Mb or more:
    libs  61.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/Rsymphony.Rcheck/00install.out’ for details.
installed size is 11.7Mb
  sub-directories of 1Mb or more:
    Lib  11.6Mb
Running ‘run_test.R’ [7s/7s]
Running the tests in ‘tests/run_test.R’ failed.
Complete output:
  > all_files <- list.files("testthat",full.names=T,pattern="*.R$")
  > 
  > sapply(all_files,source)
  Loading required package: magick
  Linking to ImageMagick 6.9.9.39
  Enabled features: cairo, fontconfig, freetype, lcms, pango, rsvg, webp
  Disabled features: fftw, ghostscript, x11
  Loading required package: XML
  Error: Test failed: 'RTestCollection write HTML summary errors'
  * `writeExecSummary.html(...)` produced warnings.
  * `writeExecSummary.html(...)` produced warnings.
  Execution halted
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    doc        1.1Mb
    libs       1.9Mb
    projects   2.7Mb
Found the following significant warnings:
  getFunctions.cpp:90:16: warning: explicitly assigning value of variable of type 'arma::mat' (aka 'Mat<double>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RTransProb.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘rtrek.Rmd’ using rmarkdown
Warning in engine$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]="webshotb5f33f4cadf8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotb5f33f4cadf8.png': No such file or directory
Quitting from lines 105-110 (rtrek.Rmd) 
Error: processing vignette 'rtrek.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘rtrek.Rmd’

SUMMARY: processing the following file failed:
  ‘rtrek.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 29.5Mb
  sub-directories of 1Mb or more:
    doc    7.8Mb
    libs  20.8Mb
Running ‘testthat.R’ [8s/8s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 581 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 30 ]
  1. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  2. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  3. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  4. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  5. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  6. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  7. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  8. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#268) 
  9. Failure: $split errors for out-of-range subsequence indices (@test-TRNG.Engine.R#264) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘mcMat.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 20-26 (mcMat.Rmd) 
Error: processing vignette 'mcMat.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/RtmpE2NZEt/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_158504d2b428/sourceCpp_2.so':
  dlopen(/private/tmp/RtmpE2NZEt/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_158504d2b428/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/RtmpE2NZEt/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_158504d2b428/sourceCpp_2.so
  Reason: image not found
--- failed re-building ‘mcMat.Rmd’

--- re-building ‘rTRNG.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Building shared library for Rcpp code chunk...
Quitting from lines 106-129 (rTRNG.Rmd) 
Error: processing vignette 'rTRNG.Rmd' failed with diagnostics:
unable to load shared object '/private/tmp/Rtmpq4zwfv/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1586d3ae4bec9/sourceCpp_2.so':
  dlopen(/private/tmp/Rtmpq4zwfv/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1586d3ae4bec9/sourceCpp_2.so, 6): Library not loaded: rTRNG.so
  Referenced from: /private/tmp/Rtmpq4zwfv/sourceCpp-x86_64-apple-darwin15.6.0-1.0.3/sourcecpp_1586d3ae4bec9/sourceCpp_2.so
  Reason: image not found
--- failed re-building ‘rTRNG.Rmd’

--- re-building ‘rTRNG.useR2017.pdf.asis’ using asis
--- finished re-building ‘rTRNG.useR2017.pdf.asis’

SUMMARY: processing the following files failed:
  ‘mcMat.Rmd’ ‘rTRNG.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    R      2.9Mb
    libs   2.5Mb
installed size is 10.8Mb
  sub-directories of 1Mb or more:
    data   3.8Mb
    libs   6.4Mb
Package suggested but not available for checking: ‘modeest’
Package unavailable to check Rd xrefs: ‘modeest’
installed size is 28.8Mb
  sub-directories of 1Mb or more:
    libs  28.1Mb
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 47.9Mb
  sub-directories of 1Mb or more:
    include   2.6Mb
    libs     45.0Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RVowpalWabbit.Rcheck/00install.out’ for details.
Found the following significant warnings:
  qwiener.c:60:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
  qwiener.c:69:12: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/RWiener.Rcheck/00install.out’ for details.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs    8.3Mb
    yacas   1.3Mb
installed size is 11.0Mb
  sub-directories of 1Mb or more:
    libs    9.1Mb
    yacas   1.3Mb
installed size is 16.3Mb
  sub-directories of 1Mb or more:
    libs  16.2Mb
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    libs   8.0Mb
No protocol specified
Namespaces in Imports field not imported from:
  ‘R6’ ‘mgcv’
  All declared Imports should be used.
Running examples in ‘sae2-Ex.R’ failed
The error most likely occurred in:

> ### Name: geo_ratios
> ### Title: Compute rates or ratios for a set of geographic entities over a
> ###   set of years
> ### Aliases: geo_ratios
> 
> ### ** Examples
> 
> require(survey)
> require(MASS)
> D <- 20 # number of domains
> T <- 5 # number of years
> samp <- 16 # number of sample cases per domain
> set.seed(1)
> # use conditional.mean=TRUE to generate true small area values
> # without sampling error
> Y.list <- mvrnormSeries(D=D, T=T, rho.dyn=.9, sigma.v.dyn=1, 
+    sigma.u.dyn=.19, sigma.e=diag(5), conditional.mean=TRUE)
> # generate sampling errors
> e <- rnorm(samp * T * D, mean=0, sd=4)
> Y <- Y.list[[2]] + tapply(e, rep(1:100, each=16), mean) 
> data <- data.frame(Y=Y, X=rep(1:T, times=D))
> # model fit with the true sampling variances
> result.dyn  <- eblupDyn(Y ~ X, D, T, vardir = diag(100), data=data)
Error in y - X %*% B_Est : non-conformable arrays
Calls: eblupDyn -> dynRYfit
Execution halted
Found the following significant warnings:
  dists.cc:4239:21: warning: explicitly assigning value of variable of type 'double' to itself [-Wself-assign]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SafeBayes.Rcheck/00install.out’ for details.
installed size is 11.9Mb
  sub-directories of 1Mb or more:
    doc    2.4Mb
    libs   8.8Mb
installed size is 15.1Mb
  sub-directories of 1Mb or more:
    libs  15.0Mb
installed size is 22.3Mb
  sub-directories of 1Mb or more:
    libs  22.2Mb
Packages suggested but not available for checking:
  'GO.db', 'GOstats', 'mixer', 'org.Sc.sgd.db'
Error(s) in re-building vignettes:
  ...
--- re-building ‘sass.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 50-51 (sass.Rmd) 
Error: processing vignette 'sass.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sass.Rmd’

SUMMARY: processing the following file failed:
  ‘sass.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘gettingstarted.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘gettingstarted.Rmd’

--- re-building ‘article.Rnw’ using knitr
Error: processing vignette 'article.Rnw' failed with diagnostics:
Running 'texi2dvi' on 'article.tex' failed.
LaTeX errors:
!pdfTeX error: pdflatex (file bbm10): Font bbm10 at 657 not found
 ==> Fatal error occurred, no output PDF file produced!
--- failed re-building ‘article.Rnw’

SUMMARY: processing the following file failed:
  ‘article.Rnw’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘dyndimred’

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/3.6/scpm.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘oligoClasses’
Packages required but not available: 'ALL', 'ConsensusClusterPlus'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.0Mb
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.
Package suggested but not available for checking: ‘seasonalview’
Package unavailable to check Rd xrefs: ‘seasonalview’
installed size is  8.2Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs   5.1Mb
Packages suggested but not available for checking:
  'flowMerge', 'flowClust', 'flowCore'
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/3.6/Segmentor3IsBack.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    libs   5.3Mb
Running examples in ‘SemNetCleaner-Ex.R’ failed
The error most likely occurred in:

> ### Name: bin2resp
> ### Title: Binary Responses to Character Responses
> ### Aliases: bin2resp
> 
> ### ** Examples
> 
> # Toy example
> raw <- open.animals[c(1:10),-c(1:3)]
> 
> # Clean and prepocess data
> clean <- textcleaner(raw, partBY = "row", dictionary = "animals")
IDs refer to row number
No protocol specified
No protocol specified
Warning in fun(libname, pkgname) : couldn't connect to display ":0"
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: textcleaner ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.0Mb
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SeqFeatR.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘airway’
Error(s) in re-building vignettes:
  ...
--- re-building ‘different_thinners.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘different_thinners.Rmd’

--- re-building ‘simulate_rnaseq.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 48-50 (simulate_rnaseq.Rmd) 
Error: processing vignette 'simulate_rnaseq.Rmd' failed with diagnostics:
there is no package called 'airway'
--- failed re-building ‘simulate_rnaseq.Rmd’

SUMMARY: processing the following file failed:
  ‘simulate_rnaseq.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 15.6Mb
  sub-directories of 1Mb or more:
    doc    6.1Mb
    libs   8.7Mb
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.3Mb
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sequenza.Rcheck/00install.out’ for details.
installed size is 17.3Mb
  sub-directories of 1Mb or more:
    libs  15.9Mb
Packages suggested but not available for checking:
  'loomR', 'SingleCellExperiment', 'MAST', 'monocle'
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    libs   7.7Mb
installed size is 187.2Mb
  sub-directories of 1Mb or more:
    doc      12.0Mb
    libs    171.2Mb
    sqlite    1.5Mb
Error(s) in re-building vignettes:
--- re-building ‘sf1.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf1.Rmd’

--- re-building ‘sf2.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf2.Rmd’

--- re-building ‘sf3.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf3.Rmd’

--- re-building ‘sf4.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf4.Rmd’

--- re-building ‘sf5.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 213-215 (sf5.Rmd) 
Error: processing vignette 'sf5.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘sf5.Rmd’

--- re-building ‘sf6.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘sf6.Rmd’

SUMMARY: processing the following file failed:
  ‘sf5.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 11.3Mb
  sub-directories of 1Mb or more:
    libs   9.9Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/sgPLS.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘SGP.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP.Rmd) 
Error: processing vignette 'SGP.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP.Rmd’

--- re-building ‘SGP_Data_Analysis.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Analysis.Rmd) 
Error: processing vignette 'SGP_Data_Analysis.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Analysis.Rmd’

--- re-building ‘SGP_Data_Preparation.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-29 (SGP_Data_Preparation.Rmd) 
Error: processing vignette 'SGP_Data_Preparation.Rmd' failed with diagnostics:
argument is of length zero
--- failed re-building ‘SGP_Data_Preparation.Rmd’

SUMMARY: processing the following files failed:
  ‘SGP.Rmd’ ‘SGP_Data_Analysis.Rmd’ ‘SGP_Data_Preparation.Rmd’

Error: Vignette re-building 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/3.6/shapes.Rcheck/00install.out’ for details.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    www   7.7Mb
installed size is 10.7Mb
  sub-directories of 1Mb or more:
    R     1.5Mb
    www   8.2Mb
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/shinyRGL.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘edgeR’
Error(s) in re-building vignettes:
  ...
--- re-building ‘getting-started.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘getting-started.Rmd’

SUMMARY: processing the following file failed:
  ‘getting-started.Rmd’

Error: Vignette re-building failed.
Execution halted
Package required but not available: ‘maftools’

Package suggested but not available for checking: ‘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/3.6/SimEUCartelLaw.Rcheck/00install.out’ for details.
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    libs   4.8Mb
installed size is 14.1Mb
  sub-directories of 1Mb or more:
    doc    1.8Mb
    libs  11.8Mb
Package suggested but not available for checking: ‘topologyGSA’
Error(s) in re-building vignettes:
  ...
--- re-building ‘simPATHy.Rmd’ using rmarkdown
Warning 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 252-258 (simPATHy.Rmd) 
Error: processing vignette 'simPATHy.Rmd' failed with diagnostics:
there is no package called 'topologyGSA'
--- failed re-building ‘simPATHy.Rmd’

SUMMARY: processing the following file failed:
  ‘simPATHy.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SimRAD.Rcheck/00install.out’ for details.
installed size is 21.4Mb
  sub-directories of 1Mb or more:
    doc    2.1Mb
    libs  18.2Mb
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    R      1.9Mb
    libs   5.8Mb
Packages unavailable to check Rd xrefs: ‘Rgraphviz’, ‘graph’
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    1.1Mb
    libs   4.5Mb
installed size is 32.4Mb
  sub-directories of 1Mb or more:
    libs  30.9Mb
Error(s) in re-building vignettes:
--- re-building ‘basics.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 29-30 (basics.Rmd) 
Error: processing vignette 'basics.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basics.Rmd’

--- re-building ‘iframes.Rmd’ using rmarkdown
Warning 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 76-87 (iframes.Rmd) 
Error: processing vignette 'iframes.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘iframes.Rmd’

--- re-building ‘pdfs.Rmd’ using rmarkdown
Warning 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 31-33 (pdfs.Rmd) 
Error: processing vignette 'pdfs.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘pdfs.Rmd’

--- re-building ‘plots.Rmd’ using rmarkdown
Warning 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 88-93 (plots.Rmd) 
Error: processing vignette 'plots.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘plots.Rmd’

--- re-building ‘shiny.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘shiny.Rmd’

SUMMARY: processing the following files failed:
  ‘basics.Rmd’ ‘iframes.Rmd’ ‘pdfs.Rmd’ ‘plots.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SmartSVA.Rcheck/00install.out’ for details.
Package suggested but not available for checking: ‘SMITIDstruct’
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/3.6/smoothAPC.Rcheck/00install.out’ for details.
installed size is 12.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   8.9Mb
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
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    extdata   3.1Mb
    libs      2.5Mb
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/3.6/snpReady.Rcheck/00install.out’ for details.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    data   1.4Mb
    doc    1.6Mb
    libs   5.5Mb
Packages suggested but not available for checking:
  'r2cytoscape', 'BiocStyle', 'hgu95av2.db', 'ALL', 'org.Hs.eg.db'
Package unavailable to check Rd xrefs: ‘ALL’
Error(s) in re-building vignettes:
--- re-building ‘SourceSet.Rmd’ using rmarkdown
Warning 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: graph
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: 'BiocGenerics'

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

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

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

    IQR, mad, sd, var, xtabs

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

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

Identifing all possible orderings..
Total run time: 1.46 secs
Identifing all possible orderings..
Total run time: 0.79 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]="webshot1036025ae8906.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot1036025ae8906.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
--- failed re-building ‘SourceSet.Rmd’

SUMMARY: processing the following file failed:
  ‘SourceSet.Rmd’

Error: Vignette re-building failed.
Execution halted
Errors in running code in vignettes:
when running code in ‘jss816.Rnw’
  ...

> print(stplot(sttdf, by = "time*id"))

> library(cshapes)
Warning in read.dcf(file.path(p, "DESCRIPTION"), c("Package", "Version")) :
  cannot open compressed file '/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/Rlib/3.6/maptools/DESCRIPTION', probable reason 'No such file or directory'

  When sourcing 'jss816.R':
Error: package 'maptools' required by 'cshapes' could not be found
Execution halted
Missing or unexported objects:
  ‘pomp::covariate_table’ ‘pomp::gillespie_hl’
installed size is 34.1Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    libs  31.7Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘intro_sparkline.Rmd’ using rmarkdown
Warning 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]="webshot4c28b900111.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot4c28b900111.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
--- failed re-building ‘intro_sparkline.Rmd’

SUMMARY: processing the following file failed:
  ‘intro_sparkline.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 16.5Mb
  sub-directories of 1Mb or more:
    libs  16.4Mb
installed size is  5.8Mb
  sub-directories of 1Mb or more:
    data   4.7Mb
    libs   1.0Mb
installed size is 11.5Mb
  sub-directories of 1Mb or more:
    doc    1.2Mb
    libs  10.0Mb
No protocol specified
Namespace in Imports field not imported from: ‘methods’
  All declared Imports should be used.
installed size is 18.2Mb
  sub-directories of 1Mb or more:
    R      5.2Mb
    doc    4.9Mb
    help   5.3Mb
    libs   1.8Mb
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/3.6/spatsurv.Rcheck/00install.out’ for details.
installed size is 19.8Mb
  sub-directories of 1Mb or more:
    libs  18.0Mb
installed size is 15.3Mb
  sub-directories of 1Mb or more:
    data   5.6Mb
    libs   9.1Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    doc    3.1Mb
    libs   3.2Mb
installed size is 24.7Mb
  sub-directories of 1Mb or more:
    libs  24.3Mb
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/3.6/sphereplot.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/3.6/SphericalCubature.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/3.6/sppmix.Rcheck/00install.out’ for details.
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    data   5.4Mb
    libs   7.3Mb
installed size is 17.2Mb
  sub-directories of 1Mb or more:
    data   3.4Mb
    libs  13.0Mb
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 57.7Mb
  sub-directories of 1Mb or more:
    libs  57.4Mb
No protocol specified

(R:18158): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:18168): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See section ‘Generic functions and methods’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:18178): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The argument of a replacement function which corresponds to the right
hand side must be named ‘value’.
No protocol specified

(R:18188): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
See chapter ‘System and foreign language interfaces’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:18216): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:18248): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
All user-level objects in a package should have documentation entries.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified

(R:18258): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:18268): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:18279): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
No protocol specified

(R:18295): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
No protocol specified
The \usage entries for S3 methods should use the \method markup and not
their full name.
See chapter ‘Writing R documentation files’ in the ‘Writing R
Extensions’ manual.
No protocol specified
  
  (R:18311): Gtk-WARNING **: gtk_disable_setlocale() must be called before gtk_init()
  No protocol specified
  Note: found 40588 marked UTF-8 strings
Running ‘testthat.R’ [6s/16s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  34: withOneRestart(expr, restarts[[1L]])
  35: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  36: with_reporter(reporter = reporter, start_end_reporter = start_end_reporter,     {        reporter$start_file(basename(path))        lister$start_file(basename(path))        source_file(path, new.env(parent = env), chdir = TRUE,             wrap = wrap)        reporter$.end_context()        reporter$end_file()    })
  37: FUN(X[[i]], ...)
  38: lapply(paths, test_file, env = env, reporter = current_reporter,     start_end_reporter = FALSE, load_helpers = FALSE, wrap = wrap)
  39: force(code)
  40: doWithOneRestart(return(expr), restart)
  41: withOneRestart(expr, restarts[[1L]])
  42: withRestarts(testthat_abort_reporter = function() NULL, force(code))
  43: with_reporter(reporter = current_reporter, results <- lapply(paths,     test_file, env = env, reporter = current_reporter, start_end_reporter = FALSE,     load_helpers = FALSE, wrap = wrap))
  44: test_files(paths, reporter = reporter, env = env, stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  45: test_dir(path = test_path, reporter = reporter, env = env, filter = filter,     ..., stop_on_failure = stop_on_failure, stop_on_warning = stop_on_warning,     wrap = wrap)
  46: test_package_dir(package = package, test_path = test_path, filter = filter,     reporter = reporter, ..., stop_on_failure = stop_on_failure,     stop_on_warning = stop_on_warning, wrap = wrap)
  47: test_check("stacomiR")
  An irrecoverable exception occurred. R is aborting now ...
installed size is 12.0Mb
  sub-directories of 1Mb or more:
    include   9.9Mb
    lib       1.9Mb
Package which this enhances but not available for checking: ‘mnlogit’
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/3.6/StatDA.Rcheck/00install.out’ for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    data   2.3Mb
    libs   4.4Mb
installed size is 13.2Mb
  sub-directories of 1Mb or more:
    libs  13.0Mb
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)
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    data   1.7Mb
    libs   2.2Mb
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    doc    2.6Mb
    libs   4.4Mb
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    R          2.1Mb
    datasets   2.6Mb
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    libs   5.5Mb
Package required but not available: ‘BSgenome.Hsapiens.UCSC.hg19’

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

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
installed size is  7.6Mb
  sub-directories of 1Mb or more:
    libs   6.9Mb
Packages suggested but not available for checking: 'limma', 'samr'
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/3.6/stream.Rcheck/00install.out’ for details.
installed size is 12.4Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs  10.0Mb
installed size is 33.2Mb
  sub-directories of 1Mb or more:
    libs  32.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/STRMPS.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/3.6/stR.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘stRvignette.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 13-17 (stRvignette.Rmd) 
Error: processing vignette 'stRvignette.Rmd' failed with diagnostics:
there is no package called 'seasonal'
--- failed re-building ‘stRvignette.Rmd’

SUMMARY: processing the following file failed:
  ‘stRvignette.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    libs   3.0Mb
Package required but not available: ‘EmiStatR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following significant warnings:
  Warning: package ‘S4Vectors’ was built under R version 3.6.1
  Warning: package ‘IRanges’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/SubVis.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
  ...
--- re-building ‘suddengains-tutorial.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 472-479 (suddengains-tutorial.Rmd) 
Error: processing vignette 'suddengains-tutorial.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘suddengains-tutorial.Rmd’

SUMMARY: processing the following file failed:
  ‘suddengains-tutorial.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.0Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Packages suggested but not available for checking: 'genefilter', 'sva'
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/3.6/supervisedPRIM.Rcheck/00install.out’ for details.
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/3.6/SuppDists.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: 'rgl_init' failed, running with rgl.useNULL = TRUE
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/suropt.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/3.6/Surrogate.Rcheck/00install.out’ for details.
No protocol specified
Namespace in Imports field not imported from: ‘rootSolve’
  All declared Imports should be used.
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    doc    2.3Mb
    help   1.0Mb
    libs   1.5Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/survHE.Rcheck/00install.out’ for details.
installed size is  8.8Mb
  sub-directories of 1Mb or more:
    R      1.0Mb
    data   3.2Mb
    doc    3.3Mb
Package unavailable to check Rd xrefs: ‘survJamda’
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/3.6/SWATmodel.Rcheck/00install.out’ for details.
Running examples in ‘switchr-Ex.R’ failed
The error most likely occurred in:

> ### Name: libManifest
> ### Title: libManifest
> ### Aliases: libManifest libManifest,missing-method libManifest,missing
> ###   libManifest,character-method libManifest,character
> ###   libManifest,SwitchrCtx-method libManifest,SwitchrCtx
> 
> ### ** Examples
> 
> man = libManifest()

Execution halted
Packages suggested but not available for checking: 'cplexAPI', 'clpAPI'
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/3.6/symbolicDA.Rcheck/00install.out’ for details.
Error(s) in re-building vignettes:
--- re-building ‘HTML.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘HTML.Rmd’

--- re-building ‘tables.Rnw’ using Sweave
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

--- finished re-building ‘tables.Rnw’

SUMMARY: processing the following file failed:
  ‘HTML.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    libs   4.1Mb
Packages suggested but not available for checking:
  'limma', 'edgeR', 'DESeq2', 'S4Vectors'
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    tklibs   4.7Mb
installed size is 37.2Mb
  sub-directories of 1Mb or more:
    libs  35.9Mb
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    apps   2.0Mb
    libs   8.7Mb
installed size is 18.3Mb
  sub-directories of 1Mb or more:
    data   2.4Mb
    libs  15.6Mb
Running examples in ‘TELP-Ex.R’ failed
The error most likely occurred in:

> ### Name: telp
> ### Title: The Base Function of This Package The Free Evocation of Words
> ###   Technique
> ### Aliases: telp
> ### Keywords: function
> 
> ### ** Examples
> 
> telp()
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: telp ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
installed size is 17.4Mb
  sub-directories of 1Mb or more:
    libs  17.1Mb
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/3.6/tensorsparse.Rcheck/00install.out’ for details.
installed size is 22.7Mb
  sub-directories of 1Mb or more:
    doc        1.0Mb
    libs       7.4Mb
    tessdata  14.1Mb
Packages suggested but not available for checking: 'Rsymphony', 'gurobi'
Running ‘testthat.R’ [22s/22s]
Running the tests in ‘tests/testthat.R’ failed.
Last 13 lines of output:
  > library(testthat)
  > library(texPreview)
  > test_check("texPreview")
  ── 1. Error: (unknown) (@test-rmd.R#7)  ────────────────────────────────────────
  pandoc version 1.12.3 or higher is required and was not found (see the help page ?rmarkdown::pandoc_available).
  Backtrace:
   1. rmarkdown::render(...)
   2. rmarkdown::pandoc_available(required_pandoc, error = TRUE)
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 35 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 1 ]
  1. Error: (unknown) (@test-rmd.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘classes.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘classes.Rmd’

--- re-building ‘kable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘kable.Rmd’

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

--- re-building ‘slickr.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 80-86 (slickr.Rmd) 
Error: processing vignette 'slickr.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘slickr.Rmd’

--- re-building ‘tests_and_coverage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tests_and_coverage.Rmd’

--- re-building ‘tex_packages.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tex_packages.Rmd’

--- re-building ‘tikz.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘tikz.Rmd’

SUMMARY: processing the following file failed:
  ‘slickr.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following significant warnings:
  GloveFitter.cpp:80:7: warning: explicitly assigning value of variable of type 'GloveFit' to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/text2vec.Rcheck/00install.out’ for details.
installed size is 11.6Mb
  sub-directories of 1Mb or more:
    data   2.7Mb
    doc    3.6Mb
    libs   4.7Mb
installed size is  5.0Mb
  sub-directories of 1Mb or more:
    libs   3.3Mb
installed size is 15.2Mb
  sub-directories of 1Mb or more:
    libs  13.7Mb
installed size is 32.2Mb
  sub-directories of 1Mb or more:
    libs  32.0Mb
Found the following significant warnings:
  ref.cpp:24:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:35:14: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:50:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
  ref.cpp:61:16: warning: explicitly assigning value of variable of type 'std::string::const_iterator' (aka '__wrap_iter<const char *>') to itself [-Wself-assign-overloaded]
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tidyxl.Rcheck/00install.out’ for details.
installed size is  9.5Mb
  sub-directories of 1Mb or more:
    libs   8.5Mb
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(s) in re-building vignettes:
--- re-building ‘Tigger-Vignette.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘Tigger-Vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘Tigger-Vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Running ‘testthat.R’ [3s/7s]
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:
  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/3.6/tkrgl.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/tkRplotR.Rcheck/00install.out’ for details.
installed size is 15.5Mb
  sub-directories of 1Mb or more:
    examples  12.1Mb
    include    2.9Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘tmod.rmd’ using rmarkdown
Warning 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 51-59 (tmod.rmd) 
Error: processing vignette 'tmod.rmd' failed with diagnostics:
there is no package called 'limma'
--- failed re-building ‘tmod.rmd’

SUMMARY: processing the following file failed:
  ‘tmod.rmd’

Error: Vignette re-building failed.
Execution halted
Packages suggested but not available for checking:
  'Rcampdf', 'Rgraphviz', 'Rpoppler', 'tm.lexicon.GeneralInquirer'
Packages unavailable to check Rd xrefs: ‘graph’, ‘Rpoppler’
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/3.6/tolerance.Rcheck/00install.out’ for details.
Packages suggested but not available for checking: 'RGtk2', 'gWidgetsRGtk2'
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/topologyGSA.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ToxicoGx.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/3.6/TPMplt.Rcheck/00install.out’ for details.
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(s) in re-building vignettes:
--- re-building ‘TourDetrackeR.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric


Attaching package: 'trackeR'

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

    append

Source : http://tile.stamen.com/toner/13/4056/2748.png
Source : http://tile.stamen.com/toner/13/4057/2748.png
Source : http://tile.stamen.com/toner/13/4056/2749.png
Source : http://tile.stamen.com/toner/13/4057/2749.png
Quitting from lines 106-108 (TourDetrackeR.Rmd) 
Error: processing vignette 'TourDetrackeR.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘TourDetrackeR.Rmd’

--- re-building ‘trackeR.Rnw’ using Sweave
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 sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Warning in sanity_checks(dat = dat, silent = silent) :
  Observations with duplicated time stamps have been removed.
Loading required package: splines
Loading required package: Matrix

Attaching package: 'fda'

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

    matplot

--- finished re-building 'trackeR.Rnw'

SUMMARY: processing the following file failed:
  ‘TourDetrackeR.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.7Mb
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/3.6/TreeLS.Rcheck/00install.out’ for details.
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    extdata   1.4Mb
    libs      9.5Mb
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/3.6/treespace.Rcheck/00install.out’ for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc   3.5Mb
installed size is 84.8Mb
  sub-directories of 1Mb or more:
    doc    4.0Mb
    libs  79.9Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘choropleth_maps_with_tricolore.Rmd’ using rmarkdown
Warning 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
--- failed re-building ‘choropleth_maps_with_tricolore.Rmd’

SUMMARY: processing the following file failed:
  ‘choropleth_maps_with_tricolore.Rmd’

Error: Vignette re-building 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/3.6/trinROC.Rcheck/00install.out’ for details.
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    libs   8.7Mb
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/3.6/TSclust.Rcheck/00install.out’ for details.
Package which this enhances but not available for checking: ‘TSodbc’
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/3.6/TSCS.Rcheck/00install.out’ for details.
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 16, 2019 10:07:08 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 16, 2019 10:07:08 AM it.bancaditalia.oss.sdmx.client.RestSdmxClient runQuery
SEVERE: Internal Server Error

  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
installed size is  9.8Mb
  sub-directories of 1Mb or more:
    data   1.2Mb
    libs   8.5Mb
Running examples in ‘TSEtools-Ex.R’ failed
The error most likely occurred in:

> ### Name: mcPrt
> ### Title: Matrix Conversion in Portfolio
> ### Aliases: mcPrt
> 
> ### ** Examples
> 
> fpath<-system.file("extdata", "sample.csv", package="TSEtools")
> asset0<-getTSE(fpath)$assets
proceeding...
[1] "URL is not responding! Try it after sometimes."
proceeding...
[1] "URL is not responding! Try it after sometimes."
proceeding...

Execution halted
Error(s) in re-building vignettes:
--- re-building ‘TSplotly.Rmd’ using rmarkdown
Warning 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: TSplotly
Loading required package: zoo

Attaching package: 'zoo'

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

    as.Date, as.Date.numeric

Loading required package: ggplot2
Loading required package: plotly

Attaching package: 'plotly'

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

    last_plot

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

    filter

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

    layout

Loading required package: forecast
PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshota8915d600bdd.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshota8915d600bdd.png': No such file or directory
Quitting from lines 99-117 (TSplotly.Rmd) 
Error: processing vignette 'TSplotly.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘TSplotly.Rmd’

SUMMARY: processing the following file failed:
  ‘TSplotly.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘Plotting_Time_Series.Rmd’ using rmarkdown
Warning 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]="webshot949b6f001931.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot949b6f001931.png': No such file or directory
Quitting from lines 39-44 (Plotting_Time_Series.Rmd) 
Error: processing vignette 'Plotting_Time_Series.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘Plotting_Time_Series.Rmd’

SUMMARY: processing the following file failed:
  ‘Plotting_Time_Series.Rmd’

Error: Vignette re-building failed.
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/TTAinterfaceTrendAnalysis.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: package ‘BiocParallel’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/ttScreening.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/3.6/TukeyRegion.Rcheck/00install.out’ for details.
Package required but not available: ‘ChemmineR’

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Found the following executable files:
  inst/examples/ko.txt
  inst/examples/ru/koi8-r.txt
  src/uchardet/test/ru/koi8-r.txt
Source packages should not contain undeclared executable files.
See section ‘Package structure’ in the ‘Writing R Extensions’ manual.
installed size is 32.7Mb
  sub-directories of 1Mb or more:
    doc         6.9Mb
    dummydata   1.4Mb
    libs       23.1Mb
Error(s) in re-building vignettes:
--- re-building ‘UKgrid_vignette.Rmd’ using rmarkdown
Warning 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]="webshot64e221e02dec.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot64e221e02dec.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
--- failed re-building ‘UKgrid_vignette.Rmd’

SUMMARY: processing the following file failed:
  ‘UKgrid_vignette.Rmd’

Error: Vignette re-building failed.
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘introduction.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 66-94 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘introduction.Rmd’

SUMMARY: processing the following file failed:
  ‘introduction.Rmd’

Error: Vignette re-building 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/3.6/ungroup.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    R      1.3Mb
    doc    1.6Mb
    libs   6.5Mb
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    libs   4.4Mb
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 22.2Mb
  sub-directories of 1Mb or more:
    libs  21.4Mb
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    libs   5.1Mb
installed size is 144.7Mb
  sub-directories of 1Mb or more:
    extdata    1.0Mb
    libs     143.2Mb
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    libs   6.5Mb
Error(s) in re-building vignettes:
--- re-building ‘basic_usage.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.

Attaching package: 'dplyr'

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

    filter, lag

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

    intersect, setdiff, setequal, union

PhantomJS not found. You can install it with webshot::install_phantomjs(). If it is installed, please make sure the phantomjs executable can be found via the PATH variable.
Warning in normalizePath(f2) :
  path[1]="webshotcf6e309706a3.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshotcf6e309706a3.png': No such file or directory
Quitting from lines 54-55 (basic_usage.Rmd) 
Error: processing vignette 'basic_usage.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘basic_usage.Rmd’

SUMMARY: processing the following file failed:
  ‘basic_usage.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   4.3Mb
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/3.6/VecStatGraphs3D.Rcheck/00install.out’ for details.
Running examples in ‘VecStatGraphs3D-Ex.R’ failed
The error most likely occurred in:

> ### Name: DrawModuleAndAngleDistribution3D
> ### Title: Graphic representation of Module and Angle Distribution.
> ### Aliases: DrawModuleAndAngleDistribution3D
> ### Keywords: graphics
> 
> ### ** Examples
> 
>    FileName<-system.file("data/XYZcoor.txt", package="VecStatGraphs3D")
>    dat<-LoadData3D(FileName, Type=1)
>    DrawModuleAndAngleDistribution3D(dat, plane="XY");
Error in structure(.External(.C_dotTclObjv, objv), class = "tclObj") : 
  [tcl] invalid command name "toplevel".
Calls: DrawModuleAndAngleDistribution3D ... tktoplevel -> tkwidget -> tcl -> .Tcl.objv -> structure
Execution halted
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/3.6/vegan3d.Rcheck/00install.out’ for details.
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    libs  17.6Mb
installed size is 27.9Mb
  sub-directories of 1Mb or more:
    libs  27.4Mb
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/3.6/vennplot.Rcheck/00install.out’ for details.
Package required but not available: ‘coRdon’

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/3.6/viromeBrowser.Rcheck/00install.out’ for details.
installed size is 28.0Mb
  sub-directories of 1Mb or more:
    libs  27.3Mb
installed size is 11.1Mb
  sub-directories of 1Mb or more:
    doc           4.3Mb
    docjs         1.4Mb
    htmlwidgets   3.9Mb
installed size is 36.9Mb
  sub-directories of 1Mb or more:
    libs  36.6Mb
installed size is  8.1Mb
  sub-directories of 1Mb or more:
    libs   7.2Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/VSE.Rcheck/00install.out’ for details.
File ‘waffect/libs/waffect.so’:
  Found ‘_rand’, possibly from ‘rand’ (C)
    Object: ‘waffect.o’

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

See ‘Writing portable packages’ in the ‘Writing R Extensions’ manual.
installed size is 58.7Mb
  sub-directories of 1Mb or more:
    libs  57.5Mb
Running examples in ‘walker-Ex.R’ failed
The error most likely occurred in:

> ### Name: plot_predict
> ### Title: Prediction intervals for walker object
> ### Aliases: plot_predict
> 
> ### ** Examples
> 
> set.seed(1)
> n <- 60
> slope <- 0.0001 + cumsum(rnorm(n, 0, sd = 0.01))
> beta <- numeric(n)
> beta[1] <- 1
> for(i in 2:n) beta[i] <- beta[i-1] + slope[i-1]
> ts.plot(beta)                
> x <- rnorm(n, 1, 0.5)
> alpha <- 2
> ts.plot(beta * x)
> 
> signal <- alpha + beta * x
> y <- rnorm(n, signal, 0.25)
> ts.plot(cbind(signal, y), col = 1:2)
> data_old <- data.frame(y = y[1:(n-10)], x = x[1:(n-10)])
> rw2_fit <- walker(y ~ 1 + 
+                     rw2(~ -1 + x,
+                         beta_prior = c(0, 10), 
+                         sigma_prior = c(0, 10), 
+                         slope_prior = c(0, 10)), 
+                   sigma_y_prior = c(0, 10), 
+                   beta_prior = c(0, 10),
+                   iter = 400, chains = 1, data = data_old)

SAMPLING FOR MODEL 'walker_lm' NOW (CHAIN 1).
Chain 1: 
Chain 1: Gradient evaluation took 0.000897 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 8.97 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1: 
Chain 1: 
Chain 1: Iteration:   1 / 400 [  0%]  (Warmup)
[1] "Error in sampler$call_sampler(args_list[[i]]) : "
[2] "  c++ exception (unknown reason)"                
error occurred during calling the sampler; sampling not done
> 
> pred <- predict(rw2_fit, newdata = data.frame(x=x[(n-9):n]))
Stan model 'walker_lm' does not contain samples.
Stan model 'walker_lm' does not contain samples.
Error in matrix(0, n_iter, 0) : non-numeric matrix extent
Calls: predict -> predict.walker_fit -> matrix
Execution halted
Error(s) in re-building vignettes:
  ...
--- re-building ‘walker.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 124-128 (walker.Rmd) 
Error: processing vignette 'walker.Rmd' failed with diagnostics:
argument of length 0
--- failed re-building ‘walker.Rmd’

SUMMARY: processing the following file failed:
  ‘walker.Rmd’

Error: Vignette re-building failed.
Execution halted
Package suggested but not available for checking: ‘bioacoustics’
Package unavailable to check Rd xrefs: ‘bioacoustics’
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    client   9.4Mb
    doc      1.0Mb
installed size is 25.2Mb
  sub-directories of 1Mb or more:
    libs  25.1Mb
Package required but not available: ‘GO.db’

Packages suggested but not available for checking:
  'org.Hs.eg.db', 'org.Mm.eg.db'

See section ‘The DESCRIPTION file’ in the ‘Writing R Extensions’
manual.
Package suggested but not available for checking: ‘AnnotationDbi’
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/3.6/WhopGenome.Rcheck/00install.out’ for details.
installed size is 10.5Mb
  sub-directories of 1Mb or more:
    libs  10.4Mb
installed size is  7.8Mb
  sub-directories of 1Mb or more:
    libs   7.0Mb
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 11.5Mb
  sub-directories of 1Mb or more:
    data  11.4Mb
Error(s) in re-building vignettes:
--- re-building ‘overview.Rmd’ using rmarkdown
Warning 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
`geom_smooth()` using method = 'loess' and formula 'y ~ x'
Warning: Removed 10 rows containing non-finite values (stat_smooth).
Warning: Removed 8 rows containing missing values (geom_point).
Warning: Removed 5 rows containing missing values (geom_path).
Warning: Removed 10 rows containing missing values (geom_point).

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: '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]="webshot13f204f5efc8.png": No such file or directory
Warning in file(con, "rb") :
  cannot open file 'webshot13f204f5efc8.png': No such file or directory
Quitting from lines 214-234 (overview.Rmd) 
Error: processing vignette 'overview.Rmd' failed with diagnostics:
cannot open the connection
--- failed re-building ‘overview.Rmd’

SUMMARY: processing the following file failed:
  ‘overview.Rmd’

Error: Vignette re-building failed.
Execution halted
Found the following notes/warnings:
  Non-staged installation was used
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/x13binary.Rcheck/00install.out’ for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    bin   4.1Mb
    lib   2.1Mb
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/3.6/x3ptools.Rcheck/00install.out’ for details.
installed size is 22.6Mb
  sub-directories of 1Mb or more:
    libs  21.7Mb
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/XGR.Rcheck/00install.out’ for details.
installed size is  7.9Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    include   3.4Mb
    libs      1.8Mb
Error(s) in re-building vignettes:
  ...
--- re-building ‘gammaproteobacteria.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 24-27 (gammaproteobacteria.Rmd) 
Error: processing vignette 'gammaproteobacteria.Rmd' failed with diagnostics:
there is no package called 'ggtree'
--- failed re-building ‘gammaproteobacteria.Rmd’

SUMMARY: processing the following file failed:
  ‘gammaproteobacteria.Rmd’

Error: Vignette re-building failed.
Execution halted
installed size is 36.3Mb
  sub-directories of 1Mb or more:
    libs  36.0Mb
Found the following significant warnings:
  Warning: package ‘mixOmics’ was built under R version 3.6.1
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/YuGene.Rcheck/00install.out’ for details.
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.6/zenplots.Rcheck/00install.out’ for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    libs   7.9Mb
Running ‘test-all.R’ [25s/47s]
Running the tests in ‘tests/test-all.R’ failed.
Last 13 lines of output:
  Loading required package: raster
  Loading required package: sp
  ── 1. Error: LoadModule works (@testLoadModule.R#15)  ──────────────────────────
  cannot open the connection
  Backtrace:
   1. base::write(...)
   2. base::cat(...)
   3. base::file(file, ifelse(append, "a", "w"))
  
  ══ testthat results  ═══════════════════════════════════════════════════════════
  [ OK: 201 | SKIPPED: 31 | WARNINGS: 10 | FAILED: 1 ]
  1. Error: LoadModule works (@testLoadModule.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Error(s) in re-building vignettes:
--- re-building ‘heatmapTable.Rmd’ using rmarkdown
Warning 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
--- finished re-building ‘heatmapTable.Rmd’

--- re-building ‘ztable.Rmd’ using rmarkdown
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
--- finished re-building ‘ztable.Rmd’

--- re-building ‘ztable_update.Rmd’ using rmarkdown
Warning 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)
--- failed re-building ‘ztable_update.Rmd’

SUMMARY: processing the following file failed:
  ‘ztable_update.Rmd’

Error: Vignette re-building failed.
Execution halted
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/adaptiveGPCA.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.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/AdMit.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/apexcharter.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'
LaTeX errors when creating PDF version.
This typically indicates Rd problems.
LaTeX errors found:
!pdfTeX error: pdflatex.EXE: fflush() failed (No space left on device)
 ==> Fatal error occurred, no output PDF file produced!
Found the following significant warnings:
  Note: possible error in 'set.seed(100, sample.kind = "Rejection")': unused argument (sample.kind = "Rejection") 
See 'd:/Rcompile/CRANpkg/local/3.5/assignR.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'.
QA: possible error in set.seed(100, sample.kind = "Rejection"): unused
  argument (sample.kind = "Rejection")
installed size is  6.7Mb
  sub-directories of 1Mb or more:
    data   3.3Mb
    libs   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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/backShift.Rcheck/00install.out' for details.
Running 'testthat.R' [6s]
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 | WARNINGS: 0 | FAILED: 1 ]
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'baseline.lowpass.R' line 4
  Warning: unable to re-encode 'baseline.medianWindow.R' line 3
  Warning: unable to re-encode 'baseline.modpolyfit.R' line 4
See 'd:/Rcompile/CRANpkg/local/3.5/baseline.Rcheck/00install.out' for details.
Packages which this enhances but not available for checking:
  'doMC' 'rPython'
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/bayesCL.Rcheck/00install.out' for details.
Packages suggested but not available for checking: 'bcmapsdata' '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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/bcrm.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/bde.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/bdl.Rcheck/00install.out' for details.
installed size is 152.5Mb
  sub-directories of 1Mb or more:
    include  151.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BiBitR.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/billboarder.Rcheck/00install.out' for details.
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
clusterplots: no visible global function definition for 'par'
clusterplots: no visible global function definition for 'rainbow'
clusterplots: no visible global function definition for 'plot'
clusterplots: no visible global function definition for 'axis'
clusterplots: no visible global function definition for 'lines'
diagplots: no visible global function definition for 'par'
diagplots: no visible global function definition for 'plot'
diagplots: no visible global function definition for 'hist'
tseriesca: no visible global function definition for 'rgamma'
tseriesca: no visible global function definition for 'runif'
tseriesca: no visible global function definition for 'dbeta'
tseriesca: no visible global function definition for 'dgamma'
tseriescm: no visible global function definition for 'rgamma'
tseriescm: no visible global function definition for 'runif'
tseriescm: no visible global function definition for 'dbeta'
tseriescm: no visible global function definition for 'dgamma'
tseriescq: no visible global function definition for 'rgamma'
tseriescq: no visible global function definition for 'runif'
tseriescq: no visible global function definition for 'dbeta'
tseriescq: no visible global function definition for 'dgamma'
Undefined global functions or variables:
  axis dbeta dgamma hist lines par plot rainbow rgamma runif
Consider adding
  importFrom("grDevices", "rainbow")
  importFrom("graphics", "axis", "hist", "lines", "par", "plot")
  importFrom("stats", "dbeta", "dgamma", "rgamma", "runif")
to your NAMESPACE file.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    R     2.7Mb
    doc   2.6Mb
loo_R2.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
loo_compare.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
loo_model_weights.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
loo_predict.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
make_conditions.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
Warning in recurse(blocks) : closing unused connection 3 ()
summary.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
theme_black.Rd: Sections \title, and \name must exist and be unique in Rd files
update.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
update.brmsfit_multiple.Rd: Sections \title, and \name must exist and be unique in Rd files
update_adterms.Rd: Sections \title, and \name must exist and be unique in Rd files
validate_newdata.Rd: Sections \title, and \name must exist and be unique in Rd files
vcov.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
waic.brmsfit.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'loo_R2.brmsfit.Rd', 'loo_compare.brmsfit.Rd', 'loo_model_weights.brmsfit.Rd', 'loo_predict.brmsfit.Rd', 'make_conditions.Rd', 'make_stancode.Rd', 'summary.brmsfit.Rd', 'theme_black.Rd', 'update.brmsfit.Rd', 'update.brmsfit_multiple.Rd', 'update_adterms.Rd', 'validate_newdata.Rd', 'vcov.brmsfit.Rd', 'waic.brmsfit.Rd'
Error in file(open = "w+", encoding = "UTF-8") : 
  cannot open the connection
Calls: <Anonymous> -> .load_package_quietly -> .try_quietly
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.
* checking  * OK
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpGGGU3g\ltx11160711a45a8/ExGaussian.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/BRugs.Rcheck/00install.out' for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.6Mb
    libs   6.0Mb
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\Rtmp08I3I6\file8d6c18ae64ca/BuyseTest.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running examples in 'c14bazAAR-Ex.R' failed
The error most likely occurred in:

> ### Name: c14_date_list
> ### Title: *c14_date_list*
> ### Aliases: c14_date_list as.c14_date_list is.c14_date_list
> ###   format.c14_date_list print.c14_date_list
> 
> ### ** Examples
> 
> # c14_date_list can be crafted manually:
> as.c14_date_list(data.frame(c14age = c(2000, 2500), c14std = c(30, 35)))
	Radiocarbon date list
	dates		2
	uncalBP		2500 <U+2015> 2000 

# A tibble: 2 x 2
  c14age c14std
   <int>  <int>
1   2000     30
2   2500     35
> 
> # The c14_date_list class is stripped if
> # you apply functions to a c14_date_list
> # that return tibbles or data.frames.
> # You have to add the class again afterwards:
> library(magrittr)
> example_c14_date_list %>%
+   dplyr::filter(sourcedb == "CALPAL") %>%
+   as.c14_date_list()
Error in value[[jvseq[[jjj]]]] : subscript out of bounds
Calls: %>% ... <Anonymous> -> clean_latlon -> [<- -> [<-.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/casebase.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/cellWise.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: possible error in 'trimws(x, which = "both", ': unused argument (whitespace = "[ \t\r\n]") 
See 'd:/Rcompile/CRANpkg/local/3.5/clean.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'.
clean_character: possible error in trimws(x, which = "both", whitespace
  = "[ \t\r\n]"): unused argument (whitespace = "[ \t\r\n]")
Running examples in 'clean-Ex.R' failed
The error most likely occurred in:

> ### Name: clean
> ### Title: Clean column data to a class
> ### Aliases: clean clean.data.frame clean_logical clean_factor
> ###   clean_numeric clean_character clean_currency clean_Date clean_POSIXct
> 
> ### ** Examples
> 
> clean_logical(c("Yes", "No"))   # English
[1]  TRUE FALSE
> clean_logical(c("Oui", "Non"))  # French
[1]  TRUE FALSE
> clean_logical(c("ya", "tidak")) # Indonesian
[1]  TRUE FALSE
> clean_logical(x = c("Positive", "Negative", "Unknown", "Some value"),
+               true = "pos", false = "neg")
[1]  TRUE FALSE    NA    NA
> 
> gender_age <- c("male 0-50", "male 50+", "female 0-50", "female 50+")
> clean_factor(gender_age, c("M", "F"))
[1] M M F F
Levels: M F
> clean_factor(gender_age, c("Male", "Female"))
[1] Male   Male   Female Female
Levels: Male Female
> clean_factor(gender_age, c("0-50", "50+"), ordered = TRUE)
[1] 0-50 50+  0-50 50+ 
Levels: 0-50 < 50+
> 
> clean_Date("13jul18", "ddmmmyy")
[1] "2018-07-13"
> clean_Date("12 august 2010")
Cleaning dates using format 'dd mmmm yyyy' ('%d %B %Y')
[1] "2010-08-12"
> clean_Date("12 06 2012")
Cleaning dates using format 'dd mm yyyy' ('%d %m %Y')
[1] "2012-06-12"
> clean_Date(36526) # Excel date
Cleaning dates using Excel format
[1] "2000-01-01"
> clean_Date("43658")
Cleaning dates using Excel format
[1] "2019-07-12"
> clean_Date("14526", "Excel") # "1939-10-08"
[1] "1939-10-08"
> 
> clean_POSIXct("Created log on 2019/04/11 11:23 by user Joe")
[1] "2019-04-11 11:23:00 CEST"
> 
> clean_numeric("qwerty123456")
[1] 123456
> clean_numeric("Positive (0.143)")
[1] 0.143
> clean_numeric("0,143")
[1] 0.143
> 
> clean_character("qwerty123456")
Error in trimws(x, which = "both", whitespace = "[ \t\r\n]") : 
  unused argument (whitespace = "[ \t\r\n]")
Calls: clean_character
Execution halted
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpSSY8ej\file2121c60ae1488/climdex.su.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Found the following significant warnings:
  Warning: unable to re-encode 'indecis_indices.R' lines 4067, 4098
See 'd:/Rcompile/CRANpkg/local/3.5/ClimInd.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

Quitting from lines 86-87 (codebook.Rmd) 
Error: processing vignette 'codebook.Rmd' failed with diagnostics:
Could not summarise item age. Error: 'skim_with_defaults' is not an exported object from 'namespace:skimr'
Execution halted
Problems with news in 'inst/NEWS.Rd':
  inst/NEWS.Rd:833: unknown macro '\proglang'
  inst/NEWS.Rd:893: unknown macro '\proglang'
  inst/NEWS.Rd:1034: unknown macro '\proglang'
  inst/NEWS.Rd:1050: unknown macro '\proglang'
  inst/NEWS.Rd:1052: unknown macro '\proglang'
  inst/NEWS.Rd:1057: unknown macro '\proglang'
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/coloc.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/comato.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
trying URL 'https://downloads.lightbend.com/scala/2.13.1/scala-2.13.1.tgz'
Content type 'application/octet-stream' length 19685743 bytes (18.8 MB)
==================================================
downloaded 18.8 MB

Quitting from lines 32-37 (commonsMath.Rmd) 
Error: processing vignette 'commonsMath.Rmd' failed with diagnostics:
Error in scalaConfig(FALSE): 

<<<<<<<<<<
<<<<<<<<<<
<<<<<<<<<<

Scala is not found!  Please run 'rscala::scalaConfig(download="scala")'

>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>>

Execution halted
Error in re-building vignettes:
  ...
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

Quitting from lines 93-94 (senate.Rmd) 
Error: processing vignette 'senate.Rmd' failed with diagnostics:
Request failed. Please check the validity of the information you requested.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/CoreGx.Rcheck/00install.out' for details.
Running 'test.R' [90s]
Running the tests in 'tests/test.R' failed.
Complete output:
  > library(testthat)
  > library(mockr)
  
  Attaching package: 'mockr'
  
  The following object is masked from 'package:testthat':
  
      with_mock
  
  > library(corehunter)
  Loading required package: rJava
  > 
  > test_check("corehunter")
  -- 1. Error: arguments are checked (@testAnalysis.R#12)  -----------------------
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   14. rlang::cnd_entrace(cnd)
   17. rJava:::`$.Throwable`(cnd, "trace")
   18. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  -- 2. Error: arguments are checked (@testData.R#532)  --------------------------
  no field, method or inner class called 'trace' 
  Backtrace:
    1. testthat::expect_error(...)
   13. rlang::cnd_entrace(cnd)
   16. rJava:::`$.Throwable`(cnd, "trace")
   17. rJava:::._jobjRef_dollar(x[["jobj"]], name)
  
  == testthat results  ===========================================================
  [ OK: 2416 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Error: arguments are checked (@testAnalysis.R#12) 
  2. Error: arguments are checked (@testData.R#532) 
  
  Error: testthat unit tests failed
  Execution halted
is_deprecated: no visible global function definition for
  'warningCondition'
Undefined global functions or variables:
  warningCondition
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/CoSMoS.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...

********************************************************
Note: As of version 1.0.0, cowplot does not change the
  default ggplot2 theme anymore. To recover the previous
  behavior, execute:
  theme_set(theme_cowplot())
********************************************************

Quitting from lines 70-73 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
no applicable method for 'depth' applied to an object of class "NULL"
Execution halted
Error in re-building vignettes:
  ...
Loading required package: rms
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

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve

Loading required package: mgcv
Loading required package: nlme
This is mgcv 1.8-31. For overview type 'help("mgcv-package")'.

Attaching package: 'dplyr'

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

    collapse

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

    src, summarize

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 81-83 (simulating_survival_data.Rmd) 
Error: processing vignette 'simulating_survival_data.Rmd' failed with diagnostics:
there is no package called 'bindrcpp'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.6/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/CRPClustering.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/CSFA.Rcheck/00install.out' for details.
Packages required and available but unsuitable versions:
  'graphics' 'grDevices' 'stats' 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [272s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(dabestr)
  Loading required package: boot
  Loading required package: magrittr
  
  Attaching package: 'magrittr'
  
  The following objects are masked from 'package:testthat':
  
      equals, is_less_than, not
  
  > 
  > test_check("dabestr")
  -- 1. Failure: Using `grp` as x column is kosher (@test-unquoting.R#50)  -------
  df_analysed.result$control_size not equal to 54.
  1/1 mismatches
  [1] 40 - 54 == -14
  
  -- 2. Failure: Using `grp` as x column is kosher (@test-unquoting.R#51)  -------
  df_analysed.result$test_size not equal to 46.
  1/1 mismatches
  [1] 60 - 46 == 14
  
  -- 3. Failure: Using `grp` as x column is kosher (@test-unquoting.R#53)  -------
  df_analysed.result$difference not equal to -0.02769726.
  1/1 mismatches
  [1] 0.0367 - -0.0277 == 0.0644
  
  -- 4. Failure: Using `grp` as x column is kosher (@test-unquoting.R#54)  -------
  round(df_analysed.result$bca_ci_low, digits = 4) not equal to -0.1253.
  1/1 mismatches
  [1] -0.0725 - -0.125 == 0.0528
  
  -- 5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55)  -------
  df_analysed.result$bca_ci_high not equal to 0.07162217.
  1/1 mismatches
  [1] 0.146 - 0.0716 == 0.0742
  
  == testthat results  ===========================================================
  [ OK: 17 | SKIPPED: 29 | WARNINGS: 0 | FAILED: 5 ]
  1. Failure: Using `grp` as x column is kosher (@test-unquoting.R#50) 
  2. Failure: Using `grp` as x column is kosher (@test-unquoting.R#51) 
  3. Failure: Using `grp` as x column is kosher (@test-unquoting.R#53) 
  4. Failure: Using `grp` as x column is kosher (@test-unquoting.R#54) 
  5. Failure: Using `grp` as x column is kosher (@test-unquoting.R#55) 
  
  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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/dae.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/DALEX.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.
Found the following significant warnings:
  Warning: unable to re-encode 'missing_value_impute.R' line 216
See 'd:/Rcompile/CRANpkg/local/3.5/DDPNA.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.
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.
installed size is 10.1Mb
  sub-directories of 1Mb or more:
    libs   7.4Mb
Running 'test-all.R' [29s]
Running the tests in 'tests/test-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > library(dendextend)
  
  ---------------------
  Welcome to dendextend version 1.12.0
  Type citation('dendextend') for how to cite the package.
  
  Type browseVignettes(package = 'dendextend') for the package vignette.
  The github page is: https://github.com/talgalili/dendextend/
  
  Suggestions and bug-reports can be submitted at: https://github.com/talgalili/dendextend/issues
  Or contact: <tal.galili@gmail.com>
  
  	To suppress this message use:  suppressPackageStartupMessages(library(dendextend))
  ---------------------
  
  
  Attaching package: 'dendextend'
  
  The following object is masked from 'package:stats':
  
      cutree
  
  > test_check("dendextend")
  Bootstrap (r = 0.4)... Done.
  Bootstrap (r = 0.6)... Done.
  Bootstrap (r = 0.8)... Done.
  Bootstrap (r = 1.0)... Done.
  Bootstrap (r = 1.2)... Done.
  Bootstrap (r = 1.4)... Done.
  -- 1. Failure: extract au (@test-pvclust_extract.R#12)  ------------------------
  round(pvclust_edges(dend)[, 3], digits = 2) not identical to c(0.97, 1, 1).
  2/3 mismatches (average diff: 0.11)
  [1] 0.76 - 0.97 == -0.21
  [2] 0.99 - 1.00 == -0.01
  
  == testthat results  ===========================================================
  [ OK: 409 | SKIPPED: 0 | WARNINGS: 4 | FAILED: 1 ]
  1. Failure: extract au (@test-pvclust_extract.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.8Mb
    help   1.4Mb
    libs   1.8Mb
Packages which this enhances but not available for checking:
  'gurobi' 'Rcplex'
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 "compiledCode.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Warning in lsoda(y, times, func, parms, ...) :
  repeated error test failures on a step, but integration was successful - singularity ?
Warning in lsoda(y, times, func, parms, ...) :
  Returning early. Results are accurate, as far as they go
Warning in lsoda(y, times, func, parms, ...) :
  an excessive amount of work (> maxsteps ) was done, but integration was not successful - increase maxsteps
Warning in lsoda(y, times, func, parms, ...) :
  Returning early. Results are accurate, as far as they go
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "deSolve.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'deSolve.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE: fflush() failed (No space left on device)
 ==> Fatal error occurred, no output PDF file produced!
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/detectRUNS.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/diffMeanVar.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/difNLR.Rcheck/00install.out' for details.
Running examples in 'DistributionOptimization-Ex.R' failed
The error most likely occurred in:

> ### Name: DistributionOptimization
> ### Title: Distribution Fitting
> ### Aliases: DistributionOptimization
> 
> ### ** Examples
> 
> DistributionOptimization(c(rnorm(200),rnorm(200,3)), 2,Iter = 15)
Loading required namespace: parallelDist
Failed with error:  'there is no package called 'parallelDist''
Error in loadNamespace(name) : there is no package called 'parallelDist'
Calls: DistributionOptimization ... tryCatch -> tryCatchList -> tryCatchOne -> <Anonymous>
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/dlstats.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'pnbeta.R' lines 12, 35
  Warning: unable to re-encode 'pnchisq.R' lines 263, 264, 265, 266, 648, 652, 654, 667, 675, 676, 716
  Warning: unable to re-encode 'qnchisq.R' lines 135, 136, 146, 147, 148, 149, 243, 248, 250
See 'd:/Rcompile/CRANpkg/local/3.5/DPQ.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/dr4pl.Rcheck/00install.out' for details.
Error in re-building vignettes:
  ...
drtmle: TMLE with doubly robust inference
Version: 1.0.4
Loading required package: nnls
Super Learner
Version: 2.0-25
Package created on 2019-08-05

Quitting from lines 1049-1062 (using_drtmle.Rmd) 
Error: processing vignette 'using_drtmle.Rmd' failed with diagnostics:
there is no package called 'snow'
Execution halted
Error in re-building vignettes:
  ...
Loading required package: proxy

Attaching package: 'proxy'

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

    as.dist, dist

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

    as.matrix

Loaded dtw v1.21-3. See ?dtw for help, citation("dtw") for use in publication.

Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "dtw.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Error: running 'texi2dvi' on 'dtw.tex' failed

LaTeX errors:
!pdfTeX error: pdflatex.EXE: fwrite() failed
 ==> Fatal error occurred, no output PDF file produced!
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/earlywarnings.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ecd.Rcheck/00install.out' for details.
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpC06zmO\file2c69479ee3714/ecd.adj_gamma.R': No space left on device
Error in file(out, "wt") : cannot open the connection
Execution halted
Running examples in 'EcoHydRology-Ex.R' failed
The error most likely occurred in:

> ### Name: get_usgs_gage
> ### Title: A function to grab daily stream flow measurements from the USGS
> ###   waterdata.usgs.gov server.
> ### Aliases: get_usgs_gage
> 
> ### ** Examples
> 
> 
> flowgage_id="04216500"
> flowgage=get_usgs_gage(flowgage_id)
Warning in file(con, "r") :
  InternetOpenUrl failed: 'Eine Umleitungsanforderung ändert eine nicht sichere in eine sichere Verbindung.'
Error in file(con, "r") : cannot open the connection
Calls: get_usgs_gage -> readLines -> file
Execution halted
Running 'testthat.R' [17s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(ECoL)
  > 
  > test_check("ECoL")
  -- 1. Failure: multiclass.result (@test_linearity.R#13)  -----------------------
  as.numeric(aux$L3) not equal to 0.01.
  1/1 mismatches
  [1] 0.00667 - 0.01 == -0.00333
  
  -- 2. Failure: multiclass.result (@test_neighborhood.R#16)  --------------------
  as.numeric(aux$N4) not equal to 0.00666667.
  1/1 mismatches
  [1] 0.0133 - 0.00667 == 0.00667
  
  == testthat results  ===========================================================
  [ OK: 97 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 2 ]
  1. Failure: multiclass.result (@test_linearity.R#13) 
  2. Failure: multiclass.result (@test_neighborhood.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
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

Quitting from lines 93-95 (EHRtemporalVariability.Rmd) 
Error: processing vignette 'EHRtemporalVariability.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/ELYP.Rcheck/00install.out' for details.
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(emba)
  > 
  > test_check("emba")
  -- 1. Failure: it returns correct results (@test-analysis.R#8)  ----------------
  count_models_that_predict_synergies(...) not equal to 25.
  1/1 mismatches
  [1] 26 - 25 == 1
  
  -- 2. Failure: it returns correct results (@test-analysis.R#10)  ---------------
  count_models_that_predict_synergies(...) not equal to 360.
  1/1 mismatches
  [1] 310 - 360 == -50
  
  -- 3. Failure: it returns correct results (@test-analysis.R#11)  ---------------
  count_models_that_predict_synergies(...) not equal to 312.
  1/1 mismatches
  [1] 334 - 312 == 22
  
  -- 4. Failure: it returns correct results (@test-analysis.R#12)  ---------------
  count_models_that_predict_synergies(...) not equal to 329.
  1/1 mismatches
  [1] 313 - 329 == -16
  
  -- 5. Failure: it returns correct results (@test-analysis.R#14)  ---------------
  count_models_that_predict_synergies(...) not equal to 119.
  1/1 mismatches
  [1] 91 - 119 == -28
  
  -- 6. Failure: it returns correct results (@test-analysis.R#15)  ---------------
  count_models_that_predict_synergies(...) not equal to 119.
  1/1 mismatches
  [1] 91 - 119 == -28
  
  == testthat results  ===========================================================
  [ OK: 19 | SKIPPED: 0 | WARNINGS: 0 | FAILED: 6 ]
  1. Failure: it returns correct results (@test-analysis.R#8) 
  2. Failure: it returns correct results (@test-analysis.R#10) 
  3. Failure: it returns correct results (@test-analysis.R#11) 
  4. Failure: it returns correct results (@test-analysis.R#12) 
  5. Failure: it returns correct results (@test-analysis.R#14) 
  6. Failure: it returns correct results (@test-analysis.R#15) 
  
  Error: testthat unit tests failed
  Execution halted
Found the following significant warnings:
  Warning: S3 methods 'print.sparseSummary', 'print.diagSummary', 'c.abIndex', 'c.sparseVector', 'as.array.Matrix', 'as.array.sparseVector', 'as.matrix.Matrix', 'as.matrix.sparseVector', 'as.vector.Matrix', 'as.vector.sparseVector' were declared in NAMESPACE but not found
See 'd:/Rcompile/CRANpkg/local/3.5/emmeans.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/emojifont.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/EnvStats.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ezsim.Rcheck/00install.out' for details.
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in .pkg2tex(files, outfile, encoding = encoding, append = append,  :
  file 'D:\temp\RtmpeqeOzf\ltx274a45d154434/plot.fanc.tex' lacks a header: skipping
Warning in .pkg2tex(files, outfile, encoding = encoding, append = append,  :
  file 'D:\temp\RtmpeqeOzf\ltx274a45d154434/select.fanc.tex' lacks a header: skipping
Error in writeLines(readLines(f), outcon) : Error writing to connection
Running massageExamples to create 'fastcox-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\RtmpQZyRJI\file213fc1524490b/cv.cocktail.R': No space left on device
Execution halted
 NONE
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/FastRWeb.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.5/fdq.Rcheck/00install.out' for details.
installed size is  6.6Mb
  sub-directories of 1Mb or more:
    data   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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/FinCal.Rcheck/00install.out' for details.
Found the following significant warnings:
  Note: possible error in 'set.seed(42, sample.kind = "Rounding")': unused argument (sample.kind = "Rounding") 
See 'd:/Rcompile/CRANpkg/local/3.5/fingertipscharts.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'.
create_test_data: possible error in set.seed(42, sample.kind =
  "Rounding"): unused argument (sample.kind = "Rounding")
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  6.4Mb
  sub-directories of 1Mb or more:
    doc    1.9Mb
    help   2.3Mb
    libs   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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/flippant.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: unable to re-encode 'isoweek.R' line 40
See 'd:/Rcompile/CRANpkg/local/3.5/FluMoDL.Rcheck/00install.out' for details.
export.Rd: Sections \title, and \name must exist and be unique in Rd files
flux-internal.Rd: Sections \title, and \name must exist and be unique in Rd files
flux-package.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
Error writing to connection:  No space left on device
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
cannot open the connection
problems found in 'export.Rd', 'flux-internal.Rd', 'flux-package.Rd', 'flux.Rd', 'flux.calib.Rd', 'fluxx.Rd', 'gflux.Rd', 'gpp.Rd', 'inspect.Rd', 'lips.Rd', 'modjust.Rd', 'plot.fluss.Rd', 'plot.gpp.Rd', 'plot.reco.Rd', 'reco.Rd', 'reco.bulk.Rd', 'round.POSIXlt.Rd', 'tbl8.Rd', 'tt.nee.Rd', 'tt.pre.Rd'
Error in re-building vignettes:
  ...
Warning: executing %dopar% sequentially: no parallel backend registered
randomForest 4.6-14
Type rfNews() to see new features/changes/bug fixes.
Warning in system(paste(shQuote(texi2dvi), if (quiet) "--quiet" else "",  :
  running command '"D:\compiler\texmf\miktex\bin\texify.exe" --quiet --pdf "foreach.tex" --max-iterations=20 -I "D:/RCompile/recent/R-3.5.3/share/texmf/tex/latex" -I "D:/RCompile/recent/R-3.5.3/share/texmf/bibtex/bst"' had status 1
Execution halted
Rd conversion errors:
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpIbrowK\ltx2fe1444867ce8/foreach.tex': No space left on device
Error in file(out, "wt") : cannot open the connection
Running 'testthat.R' [217s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [185s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > Sys.setenv("R_TESTS" = "")
  > if (require(testthat)) {
  +   test_check("forecast")
  + }
  Loading required package: testthat
  Loading required package: forecast
  -- 1. Error: tests for autoplot/gg functions (@test-ggplot.R#64)  --------------
  need at least two non-NA values to interpolate
  Backtrace:
   1. forecast::ggseasonplot(...)
   2. ggplot2::scale_color_gradientn(colours = col)
   5. scales::gradient_n_pal(colours, values, space)
   6. scales::colour_ramp(colours)
   7. stats::approxfun(x_in, lab_in[, 1])
  
  == testthat results  ===========================================================
  [ OK: 774 | SKIPPED: 5 | WARNINGS: 1 | FAILED: 1 ]
  1. Error: tests for autoplot/gg functions (@test-ggplot.R#64) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  The vignette engine knitr::rmarkdown is not available, because the rmarkdown package is not installed. Please install it.
Quitting from lines 896-920 (Vignette.Rmd) 
Error: processing vignette 'Vignette.Rmd' failed with diagnostics:
could not find function "doColorRamp"
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 43-49 (pcl-vignette.Rmd) 
Error: processing vignette 'pcl-vignette.Rmd' failed with diagnostics:
need at least two non-NA values to interpolate
Execution halted
Packages suggested but not available for checking:
  'Rsocp' 'Rnlminb2' 'Rdonlp2'
Check process probably crashed or hung up for 20 minutes ... killed
Most likely this happened in the example checks (?),
if not, ignore the following last lines of example output:
 5 0.290 Prem~ I     VS2      62.4    58   334  4.2   4.23  2.63
 6 0.24  Very~ J     VVS2     62.8    57   336  3.94  3.96  2.48
 7 0.24  Very~ J     VVS2     62.8    57   336  3.94  3.96  2.48
 8 0.24  Very~ I     VVS1     62.3    57   336  3.95  3.98  2.47
 9 0.24  Very~ I     VVS1     62.3    57   336  3.95  3.98  2.47
10 0.26  Very~ H     SI1      61.9    55   337  4.07  4.11  2.53
# ... with 74,897 more rows, and 2 more variables: approximate_name <chr>,
#   type <int>
> 
> 
> 
> 
> ### * <FOOTER>
> ###
> cleanEx()

detaching 'package:ggplot2', 'package:dplyr'

> options(digits = 7L)
> base::cat("Time elapsed: ", proc.time() - base::get("ptime", pos = 'CheckExEnv'),"\n")
Time elapsed:  18.12 0.84 20.13 NA NA 
> grDevices::dev.off()
null device 
          1 
> ###
> ### Local variables: ***
> ### mode: outline-minor ***
> ### outline-regexp: "\\(> \\)?### [*]+" ***
> ### End: ***
> quit('no')
======== End of example output (where/before crash/hang up occured ?) ========
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/gameofthrones.Rcheck/00install.out' for details.
AICc.Rd: Sections \title, and \name must exist and be unique in Rd files
cv.gamlr.Rd: Sections \title, and \name must exist and be unique in Rd files
Error writing to connection:  No space left on device
hockey.Rd: Sections \title, and \name must exist and be unique in Rd files
problems found in 'AICc.Rd', 'cv.gamlr.Rd', 'gamlr.Rd', 'hockey.Rd'
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
Warning in close.connection(con) :
  Problem closing connection:  No space left on device
lms: no visible global function definition for 'str2lang'
Undefined global functions or variables:
  str2lang
Warning in file(out, "wt") :
  cannot open file 'D:\temp\RtmpmqE6jA\file1876457ec3d73/plot.cv.gamsel.R': No space left on device
Error in file(out, "wt") : cannot open the connection
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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/gapfill.Rcheck/00install.out' for details.
Running massageExamples to create 'geomapdata-Ex.R' failed
Error in file(out, "wt") : cannot open the connection
Calls: <Anonymous> -> Rd2ex -> file
In addition: Warning message:
In file(out, "wt") :
  cannot open file 'D:\temp\RtmpqaLDp7\file418c41077b4a/geomapdata-package.R': No space left on device
Execution halted
 NONE
Running 'testthat.R' [29s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(raster)
  Loading required package: sp
  > library(sp)
  > library(sf)
  Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
  > 
  > test_check("geometr")
  Loading required package: geometr
  -- 1. Failure: transform from geom to grob (@test_gc_grob.R#25)  ---------------
  Check on names(polyGrob[[1]]) isn't true.
  Must be a permutation of set {x,y,id,id.lengths,pathId,pathId.lengths,rule,name,gp,vp}
  
  Reading layer `nc' from data source `D:\temp\RtmpYnbglQ\RLIBS_1ddc5f871029\sf\shape\nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  == testthat results  ===========================================================
  [ OK: 695 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 1 ]
  1. Failure: transform from geom to grob (@test_gc_grob.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [31s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(checkmate)
  > library(raster)
  Loading required package: sp
  > library(sp)
  > library(sf)
  Linking to GEOS 3.6.1, GDAL 2.2.3, PROJ 4.9.3
  > 
  > test_check("geometr")
  Loading required package: geometr
  -- 1. Failure: transform from geom to grob (@test_gc_grob.R#25)  ---------------
  Check on names(polyGrob[[1]]) isn't true.
  Must be a permutation of set {x,y,id,id.lengths,pathId,pathId.lengths,rule,name,gp,vp}
  
  Reading layer `nc' from data source `D:\temp\RtmpYnbglQ\RLIBS_1ddc5f871029\sf\shape\nc.shp' using driver `ESRI Shapefile'
  Simple feature collection with 100 features and 14 fields
  geometry type:  MULTIPOLYGON
  dimension:      XY
  bbox:           xmin: -84.32385 ymin: 33.88199 xmax: -75.45698 ymax: 36.58965
  epsg (SRID):    4267
  proj4string:    +proj=longlat +datum=NAD27 +no_defs
  == testthat results  ===========================================================
  [ OK: 695 | SKIPPED: 0 | WARNINGS: 8 | FAILED: 1 ]
  1. Failure: transform from geom to grob (@test_gc_grob.R#25) 
  
  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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/gganimate.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggbeeswarm.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggcorrplot.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggdendro.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggetho.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggfittext.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.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_tibble.grouped_df', 'as_tibble.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', 'distinct_.tbl_df', 'do.NULL', 'do.da [... truncated]
See 'd:/Rcompile/CRANpkg/local/3.5/ggforce.Rcheck/00install.out' for details.