Error in re-building vignettes:
  ...
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Warning in rbind(riverTouch, slot(river, "data")["OBJECTID"][[1]]) :
  number of columns of result is not a multiple of vector length (arg 2)
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Watersheds.tex' failed.
LaTeX errors:
! LaTeX Error: File `apacite.sty' not found.

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

! Emergency stop.
<read *> 
         
l.14 \bibliographystyle
                       {apacite}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Content type 'unknown' length 1513796 bytes (1.4 MB)
==================================================
downloaded 1.4 MB

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

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

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

! Emergency stop.
<read *> 
         
l.158 \endinput
               ^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
 [>] 490 sequences in the data set
 [>] min/max sequence length: 70/70
 [>] 490 sequences with 6 distinct states
 [>] creating a 'sm' with a single substitution cost of 1
 [>] creating 6x6 substitution-cost matrix using 1 as constant value
 [>] 490 distinct sequences
 [>] min/max sequence length: 70/70
 [>] computing distances using the HAM metric
 [>] elapsed time: 0.17 secs
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'WeightedClusterPreview.tex' failed.
LaTeX errors:
! LaTeX Error: File `subfigure.sty' not found.

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

! Emergency stop.
<read *> 
         
l.78 \usepackage
                {afterpage}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'Definition.tex' failed.
LaTeX errors:
! LaTeX Error: File `fullpage.sty' not found.

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

! Emergency stop.
<read *> 
         
l.4 \usepackage
               {verbatim}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package required but not available: ‘GO.db’

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

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

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

! Emergency stop.
<read *> 
         
l.12 \usepackage
                {wasysym}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘genefilter’
Unexported objects imported by ':::' calls:
  ‘circular:::DensityCircularRad’ ‘circular:::DvonmisesRad’
  ‘circular:::DwrappednormalRad’ ‘circular:::MlevonmisesRad’
  ‘circular:::MlewrappednormalRad’
  See the note in ?`:::` about the use of this operator.
Error in re-building vignettes:
  ...
Warning in engine$weave(file, quiet = quiet, encoding = enc) :
  Pandoc (>= 1.12.3) and/or pandoc-citeproc not available. Falling back to R Markdown v1.
Quitting from lines 53-54 (Automat.Rmd) 
Error: processing vignette 'Automat.Rmd' failed with diagnostics:
cannot open the connection
Execution halted
installed size is  6.1Mb
  sub-directories of 1Mb or more:
    libs   5.4Mb
Error in re-building vignettes:
  ...
Error: processing vignette 'wrappedvig.ltx' failed with diagnostics:
Running 'texi2dvi' on 'wrappedvig.ltx' failed.
LaTeX errors:
! Package pdftex.def Error: File `wrappedv1-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv2-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv3-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                                              
! Package pdftex.def Error: File `wrappedv4-eps-converted-to.pdf' not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
 ...                
Execution halted
Error in re-building vignettes:
  ...
See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/soccer2-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/goggles-plot1-1-eps-converted-to.pdf' 
not found.

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
! Package pdftex.def Error: File `figure/swim-plot1-1-eps-converted-to.pdf' not
 found.

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

See the pdftex.def package documentation for explanation.
Type  H <return>  for immediate help.
!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is 13.4Mb
  sub-directories of 1Mb or more:
    libs  12.8Mb
Package suggested but not available for checking: ‘GenomicScores’
Error in re-building vignettes:
  ...
Loading required package: Xmisc

Attaching package: ‘Xmisc’

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

    dir.exists

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

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

! Emergency stop.
<read *> 
         
l.10 ^^M
        
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
installed size is  7.5Mb
  sub-directories of 1Mb or more:
    exampleData   1.6Mb
    examples      4.6Mb
Error in re-building vignettes:
  ...
Warning: running command 'kpsewhich framed.sty' had status 1
Warning in test_latex_pkg("framed", system.file("misc", "framed.sty", package = "knitr")) :
  unable to find LaTeX package 'framed'; will use a copy from knitr
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'OtherPackagesGallery.tex' failed.
LaTeX errors:
! LaTeX Error: File `titlesec.sty' not found.

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

! Emergency stop.
<read *> 
         
l.67 \usepackage
                {hyperref} % hyperref last^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Package suggested but not available for checking: ‘MBESS’
Running examples in ‘yhat-Ex.R’ failed
The error most likely occurred in:

> ### Name: aps
> ### Title: All Possible Subsets Regression
> ### Aliases: aps
> ### Keywords: models regression
> 
> ### ** Examples
> 
>   ## APS regression predicting miles per gallon based 
>   ## on vehicle weight, type of 
>   ## carborator, & number of engine cylinders
>      apsOut<-aps(mtcars,"mpg",list("wt","carb","cyl"))
> 
>   ## APS regression predicting paragraph comprehension based 
>   ## on thre verbal tests: general info, sentence comprehension,
>   ## & word classification
>  
>   ## Use HS dataset in MBESS 
>      require ("MBESS")
Loading required package: MBESS
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called ‘MBESS’
>      data(HS.data)
Warning in data(HS.data) : data set ‘HS.data’ not found
>   ## APS
>      apsOut<-aps(HS.data,"paragrap",list("general","sentence",
+                                          "wordc"))
Error in is.data.frame(x) : object 'HS.data' not found
Calls: aps -> colnames -> is.data.frame
Execution halted
Package suggested but not available for checking: ‘loon’
Error in re-building vignettes:
  ...
Error in texi2dvi(file = file, pdf = TRUE, clean = clean, quiet = quiet,  : 
  Running 'texi2dvi' on 'zipfr-tutorial.tex' failed.
LaTeX errors:
! LaTeX Error: File `vmargin.sty' not found.

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

! Emergency stop.
<read *> 
         
l.13 \setpapersize
                  [portrait]{A4}^^M
!  ==> Fatal error occurred, no output PDF file produced!
Calls: buildVignettes -> texi2pdf -> texi2dvi
Execution halted
Installation failed.
See ‘/Volumes/SSD-Data/Builds/R-dev-web/QA/Simon/packages/el-capitan-x86_64/results/3.4/zstdr.Rcheck/00install.out’ for details.
Found the following significant warnings:
  Warning: D:/temp/RtmpcpzNYf/R.INSTALLb1d06f9c2fed/ACEt/man/ACEt-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/ACEt.Rcheck/00install.out' for details.
prepare_Rd: ACEt-package.Rd:1: All text must be in a section
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/AER.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Anders Hedenström [fnd]
Package suggested but not available for checking: 'gge'
Running examples in 'agridat-Ex.R' failed
The error most likely occurred in:

> ### Name: crossa.wheat
> ### Title: Multi-environment trial of wheat for 18 genotypes at 25
> ###   locations
> ### Aliases: crossa.wheat
> ### Keywords: datasets
> 
> ### ** Examples
> 
> 
> data(crossa.wheat)
> dat <- crossa.wheat
> 
> # AMMI biplot.  Fig 3 of Crossa et al.
> if(require(agricolae)){
+   m1 <- with(dat, AMMI(E=loc, G=gen, R=1, Y=yield))
+   b1 <- m1$biplot[,1:4]
+   b1$PC1 <- -1 * b1$PC1 # Flip vertical
+   plot(b1$yield, b1$PC1, cex=0.0,
+        text(b1$yield, b1$PC1, cex=.5, labels=row.names(b1),col="brown"),
+        main="crossa.wheat AMMI biplot", xlab="Average yield", ylab="PC1", frame=TRUE)
+   mn <- mean(b1$yield)
+   abline(h=0, v=mn, col='wheat')
+ 
+   g1 <- subset(b1,type=="GEN")
+   text(g1$yield, g1$PC1, rownames(g1), col="darkgreen", cex=.5)
+ 
+   e1 <- subset(b1,type=="ENV")
+   arrows(mn, 0,
+          0.95*(e1$yield - mn) + mn, 0.95*e1$PC1,
+          col= "brown", lwd=1.8,length=0.1)
+ }
Loading required package: agricolae
> 
> # GGB example
> library(agridat)
> data(crossa.wheat)
> dat2 <- crossa.wheat
> 
> # FIXME: The loc grouping is now in the data
> 
> # Define mega-environment groups of locations
> dat2$eg <- ifelse(is.element(dat2$loc,
+                              c("KN","NB","PA","BJ","IL","TC",
+                                "JM","PI","AS","ID","SC","SS",
+                                "SJ","MS","MG","MM")), "Grp1", "Grp2")
> 
> library(gge)
Error in library(gge) : there is no package called 'gge'
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ARTool.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ART.Rcheck/00install.out' for details.
Package required and available but unsuitable version: 'arules'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 14.7Mb
  sub-directories of 1Mb or more:
    bin   12.0Mb
    misc   2.1Mb
Package suggested but not available for checking: 'trtf'
Found the following significant warnings:
  driver.c:381:26: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/audio.Rcheck/00install.out' for details.
installed size is 67.3Mb
  sub-directories of 1Mb or more:
    java  67.2Mb
File 'aylmer/libs/i386/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'
File 'aylmer/libs/x64/aylmer.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'aylmer.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'aylmer.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Found the following significant warnings:
  Warning: replacing previous import 'spam::det' by 'Matrix::det' when loading 'bamlss'
See 'd:/Rcompile/CRANpkg/local/3.3/bamlss.Rcheck/00install.out' for details.
installed size is 33.4Mb
  sub-directories of 1Mb or more:
    libs  32.9Mb
Running 'testthat.R' [17s]
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: 3 SKIPPED: 0 FAILED: 1
  1. Failure: (unknown) (@test-check_urls.R#25) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BayClone2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/bayesCL.Rcheck/00install.out' for details.
File 'BayesSAE/libs/i386/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'
File 'BayesSAE/libs/x64/BayesSAE.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'HBsae.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Authors@R field gives persons with no valid roles:
  Bea Hernández [rev] (Bea reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
  Elaine McVey [rev] (Elaine reviewed the package for ropensci, see https://github.com/ropensci/onboarding/issues/116)
Running 'testthat.R' [74s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  4: withr::with_output_sink(temp, withCallingHandlers(withVisible(code), warning = handle_warning, 
         message = handle_message))
  5: force(code)
  6: withCallingHandlers(withVisible(code), warning = handle_warning, message = handle_message)
  7: withVisible(code)
  8: eval_bare(get_expr(quo), get_env(quo))
  9: store_bikedata(data_dir = tempdir(), bikedb = bikedb, quiet = TRUE)
  10: rcpp_import_stn_df(bikedb, lo_stns, "lo")
  
  == testthat results  ===========================================================
  OK: 139 SKIPPED: 1 FAILED: 1
  1. Error: write and store data (@test-store-data.R#44) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
             stop("Function ", name, " not found in environment ", environmentName(env), 
                 ".", call. = FALSE)
         mock(name = name, env = env, new = eval(new_values[[qual_name]], eval_env, eval_env))
     })
  4: FUN(X[[i]], ...)
  5: stop("Can't mock functions in base packages (", pkg_name, ")", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 3
  1. Error: canDownloadFiles (@test-download_files.R#9) 
  2. Error: canReturnEmptyDFWhenEmptyDownloadFiles (@test-download_files.R#27) 
  3. Error: canProcessYaml (@test-process_yaml.R#7) 
  
  Error: testthat unit tests failed
  Execution halted
Package required and available but unsuitable version: 'csaw'

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

> ### Name: install.bioinfo
> ### Title: Download and install biology software or database
> ### Aliases: install.bioinfo
> 
> ### ** Examples
> 
> db <- sprintf('%s/.BioInstaller', tempdir())
> set.biosoftwares.db(db)
> install.bioinfo('bwa', show.all.versions = TRUE)
INFO [2018-04-02 21:59:06] Fetching bwa versions....
Error in function (type, msg, asError = TRUE)  : 
  error:1407742E:SSL routines:SSL23_GET_SERVER_HELLO:tlsv1 alert protocol version
Calls: install.bioinfo ... getURL -> curlPerform -> .Call -> <Anonymous> -> fun
Execution halted
Running 'testthat.R' [42s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  trying URL 'ftp://ftp.sjtu.edu.cn/pub/CPAN/clpa//index.html'
  ...
  downloaded 3574 bytes
  
  == testthat results  ===========================================================
  OK: 59 SKIPPED: 0 FAILED: 5
  1. Error: install.github (@test_install.R#10) 
  2. Error: install.bioinfo (@test_install.R#57) 
  3. Error: initial (@test_install_uilts.R#39) 
  4. Error: dependence (@test_install_uilts.R#88) 
  5. Error: git.download (@test_install_uilts.R#102) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'bmrm-Ex.R' failed
The error most likely occurred in:

> ### Name: mmc
> ### Title: Convenient wrapper function to solve max-margin clustering
> ###   problem on a dataset
> ### Aliases: mmc
> 
> ### ** Examples
> 
>    # -- Prepare a 2D dataset to cluster with an intercept
>    x <- cbind(intercept=100,scale(data.matrix(iris[c(1,3)]),center=TRUE,scale=FALSE))
> 
>    # -- Find max-margin clusters
>    y <- mmc(x,k=3,LAMBDA=0.001,minClusterSize=10,seeds=5)
Error in fix.by(by.y, y) : 'by' must specify a uniquely valid column
Calls: mmc ... merge.default -> merge -> merge.data.frame -> fix.by
Execution halted
Package suggested but not available for checking: 'ASGS.foyer'
Authors@R field gives persons with no valid roles:
  Brooke Anderson <brooke.anderson@colostate.edu> [rev] (0000-0002-5012-9035)
Running examples in 'BrailleR-Ex.R' failed
The error most likely occurred in:

> ### Name: ScatterPlot
> ### Title: Create a standard scatter plot with a few extra elements added
> ###   to the output object
> ### Aliases: FittedLinePlot ScatterPlot plot.scatterplot
> ###   plot.fittedlineplot print.scatterplot print.fittedlineplot
> 
> ### ** Examples
> 
> attach(airquality)
> op = par(mfcol=c(3,2))
> plot(Wind, Ozone, pch=4)
> test1 = ScatterPlot(Wind, Ozone, pch=4)
> test1 #does the plot method work?
> plot(Wind, Ozone)
> abline(coef(lm(Ozone~Wind)), col=4)
> test2 = FittedLinePlot(Wind, Ozone, line.col=4)
Error in as.list(x[setdiff(names(x), ToRemove)]) : 
  attempt to set an attribute on NULL
Calls: FittedLinePlot -> .GrabExtraArgs -> as.list
Execution halted
Running examples in 'broom-Ex.R' failed
The error most likely occurred in:

> ### Name: kde_tidiers
> ### Title: Tidy a kernel density estimate object from the ks package
> ### Aliases: kde_tidiers tidy.kde
> 
> ### ** Examples
> 
> 
> if (require("ks", quietly = TRUE)) {
+   dat <- replicate(2, rnorm(100))
+   k <- kde(dat)
+   
+   td <- tidy(k)
+   head(td)
+   
+   library(ggplot2)
+   ggplot(td, aes(x1, x2, fill = estimate)) +
+     geom_tile() +
+     theme_void()
+   
+   # also works with 3 dimensions
+   dat3 <- replicate(3, rnorm(100))
+   k3 <- kde(dat3)
+   
+   td3 <- tidy(k3)
+   head(td3)
+ }
Note: method with signature 'Matrix#diagonalMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#ddiMatrix'.
 "sparseMatrix#ANY" would also be valid
Note: method with signature 'dsparseMatrix#dsparseMatrix' chosen for function 'kronecker',
 target signature 'dgCMatrix#dtTMatrix'.
 "sparseMatrix#TsparseMatrix" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: kde -> Hpi -> gdscalar -> norm -> norm
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/BSPADATA.Rcheck/00install.out' for details.
installed size is  7.1Mb
  sub-directories of 1Mb or more:
    libs   5.9Mb
File 'camel/libs/i386/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'
File 'camel/libs/x64/camel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'SFGen.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'SFGen.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
The following files look like leftovers/mistakes:
  'Causata-vignette.log'
Please remove them from your package.
The following directory looks like a leftover from 'knitr':
  'figure'
Please remove from your package.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ChainLadder.Rcheck/00install.out' for details.
Running 'test-all.R' [26s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  checkpoint: Part of the Reproducible R Toolkit from Microsoft
  https://mran.microsoft.com/documents/rro/reproducibility/
  -- 1. Failure: is.404 (@test-0-is-404.R#11)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot") isn't false.
  
  -- 2. Failure: is.404 (@test-0-is-404.R#14)  -----------------------------------
  is.404("http://mran.microsoft.com/snapshot/2015-05-01") isn't false.
  
  == testthat results  ===========================================================
  OK: 60 SKIPPED: 7 FAILED: 2
  1. Failure: is.404 (@test-0-is-404.R#11) 
  2. Failure: is.404 (@test-0-is-404.R#14) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is 17.9Mb
  sub-directories of 1Mb or more:
    data  17.9Mb
regularize.values: possible error in xy.coords(x, y, setLab = FALSE):
  unused argument (setLab = FALSE)
Running 'testthat.R' [163s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clubSandwich)
  > set.seed(20161201)
  > test_check("clubSandwich")
  -- 1. Error: (unknown) (@test_Wald.R#4)  ---------------------------------------
  object 'Duncan' not found
  1: sample(LETTERS[1:8], size = nrow(Duncan), replace = TRUE) at testthat/test_Wald.R:4
  2: sample.int(length(x), size, replace, prob)
  3: nrow(Duncan)
  
  == testthat results  ===========================================================
  OK: 620 SKIPPED: 6 FAILED: 1
  1. Error: (unknown) (@test_Wald.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'SingleCellExperiment'
Unknown package 'SingleCellExperiment' in Rd xrefs
Warning in library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE,  :
  there is no package called 'SingleCellExperiment'
Error in .requirePackage(package) : 
  unable to find required package 'SingleCellExperiment'
Calls: <Anonymous> ... withCallingHandlers -> is -> getClassDef -> .requirePackage
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(clustree)
  Loading required package: ggraph
  Loading required package: ggplot2
  > 
  > test_check("clustree")
  -- 1. Error: SingleCellExperiment interface works (@test-clustree.R#12)  -------
  unable to find required package 'SingleCellExperiment'
  1: expect_is(clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters"), c("gg", "ggplot")) at testthat/test-clustree.R:12
  2: quasi_label(enquo(object), label)
  3: eval_bare(get_expr(quo), get_env(quo))
  4: clustree(sim_sc3, prefix = "sc3_", suffix = "_clusters")
  5: .extendsForS3(structure("SingleCellExperiment", package = "SingleCellExperiment"))
  6: extends(Class, maybe = FALSE)
  7: getClassDef(class1)
  8: .requirePackage(package)
  9: stop(gettextf("unable to find required package %s", sQuote(package)), domain = NA)
  
  == testthat results  ===========================================================
  OK: 31 SKIPPED: 0 FAILED: 1
  1. Error: SingleCellExperiment interface works (@test-clustree.R#12) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Anna Krystalli [rev] (0000-0002-2378-4915)
  Toph Allen [rev] (0000-0003-4580-091X)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/cometExactTest.Rcheck/00install.out' for details.
Packages required and available but unsuitable versions: 'graphics' 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is 10.3Mb
  sub-directories of 1Mb or more:
    R     1.8Mb
    doc   6.5Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/CovSelHigh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cplexAPI.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/CrypticIBDcheck.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/cudaBayesreg.Rcheck/00install.out' for details.
Running 'testthat.R' [101s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cutpointr)
  > 
  > test_check("cutpointr")
  -- 1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `my`.
  1/1 mismatches
  [1] 4.89 - 4.89 == 1e-04
  
  -- 2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `my`.
  1/1 mismatches
  [1] 4.89 - 4.89 == 1e-04
  
  -- 3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `myf`.
  1/1 mismatches
  [1] 4.78 - 4.78 == 2e-04
  
  -- 4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451)  -
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  -- 5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `myf`.
  1/1 mismatches
  [1] 4.78 - 4.78 == 2e-04
  
  -- 6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468)  -
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [120s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(cutpointr)
  > 
  > test_check("cutpointr")
  -- 1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `my`.
  1/1 mismatches
  [1] 4.89 - 4.89 == 1e-04
  
  -- 2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `my`.
  1/1 mismatches
  [1] 4.89 - 4.89 == 1e-04
  
  -- 3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `myf`.
  1/1 mismatches
  [1] 4.78 - 4.78 == 2e-04
  
  -- 4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451)  -
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  -- 5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464)  -
  s$desc_by_class[[1]]["yes", "Mean"] not equal to `myf`.
  1/1 mismatches
  [1] 4.78 - 4.78 == 2e-04
  
  -- 6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468)  -
  s$desc_by_class[[2]]["yes", "Mean"] not equal to `mym`.
  1/1 mismatches
  [1] 5.22 - 5.22 == -2e-04
  
  == testthat results  ===========================================================
  OK: 316 SKIPPED: 0 FAILED: 6
  1. Failure: Summary by class returns correct stats (@test-cutpointr.R#426) 
  2. Failure: Summary by class returns correct stats (@test-cutpointr.R#439) 
  3. Failure: Summary by class returns correct stats (@test-cutpointr.R#447) 
  4. Failure: Summary by class returns correct stats (@test-cutpointr.R#451) 
  5. Failure: Summary by class returns correct stats (@test-cutpointr.R#464) 
  6. Failure: Summary by class returns correct stats (@test-cutpointr.R#468) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Cyclops.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  R Consortium [fnd]
Running examples in 'ddeploy-Ex.R' failed
The error most likely occurred in:

> ### Name: duke_deploy
> ### Title: Deploy model using REST API
> ### Aliases: duke_deploy
> 
> ### ** Examples
> 
> duke_auth <- list(
+ user_name = "try_it",
+ api_key   = "db1542b66f16aba5768d8a19c27dec4facf9168a",
+ endpoint = "/api/v1.0"
+ )
> example_data <- as.data.frame(cbind(gl(3,50),rnorm(150)));names(example_data) <- c("x","y")
> example_fit  <- lm(y~x,data=example_data)
> duke_deploy(auth_details=duke_auth,model_object=example_fit)
Error: lexical error: invalid char in json text.
                                       <html>  <head><title>502 Bad Ga
                     (right here) ------^
Execution halted
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  -- 4. Failure: DCF reader works (@test-read.R#9)  ------------------------------
  desc$get("Author") not equal to c(Author = "Gábor Csárdi").
  1/1 mismatches
  x[1]: "GÃ¡bor CsÃ¡rdi"
  y[1]: "Gábor Csárdi"
  
  == testthat results  ===========================================================
  OK: 348 SKIPPED: 0 FAILED: 4
  1. Failure: get_maintainer is OK, too (@test-authors.R#171) 
  2. Failure: get works (@test-queries.R#9) 
  3. Failure: get_or_fail works (@test-queries.R#18) 
  4. Failure: DCF reader works (@test-read.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'has-devel.R' [2s]
  Running 'test-that.R' [99s]
Running the tests in 'tests/test-that.R' failed.
Last 13 lines of output:
      setup
  
  -- 1. Failure: remote_sha.github_remote returns expected value if remote does ex
  remote_sha(github_remote("hadley/devtools@v1.8.0")) not equal to "ad9aac7b9a522354e1ff363a86f389e32cec181b".
  1/1 mismatches
  x[1]: NA
  y[1]: "ad9aac7b9a522354e1ff363a86f389e32cec181b"
  
  
  == testthat results  ===========================================================
  OK: 399 SKIPPED: 10 FAILED: 1
  1. Failure: remote_sha.github_remote returns expected value if remote does exist (@test-remotes.r#75) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'AESTest.R' [0s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [1s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [0s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
Running 'AESTest.R' [0s]
  Comparing 'AESTest.Rout' to 'AESTest.Rout.save' ... OK
  Running 'digestTest.R' [0s]
  Comparing 'digestTest.Rout' to 'digestTest.Rout.save' ... OK
  Running 'hmacTest.R' [0s]
  Comparing 'hmacTest.Rout' to 'hmacTest.Rout.save' ... OK
  Running 'load-unload.R' [0s]
  Running 'num2hexTest.R' [0s]
  Running 'sha1Test.R' [1s]
Running the tests in 'tests/sha1Test.R' failed.
Last 13 lines of output:
  +         sha1(matrix(integer(0))),
  +         sha1(matrix(numeric(0)))
  +     )
  + )
  > 
  > if (getRversion() < "3.5.0") {
  +     stopifnot(
  +         identical(
  +             sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc", NULL)),
  +             "93ab6a61f1a2ad50d4bf58396dc38cd3821b2eaf"
  +         )
  +     )
  + }
  Error: identical(sha1(serialize("e13485e1b995f3e36d43674dcbfedea08ce237bc",  .... is not TRUE
  Execution halted
package 'diversitree' exists but was not installed under R >= 2.10.0 so xrefs cannot be checked
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DistatisR.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/diversitree.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/DJL.Rcheck/00install.out' for details.
File 'DPpackage/libs/i386/DPpackage.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o'
File 'DPpackage/libs/x64/DPpackage.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Objects: 'DPdensityreg.o', 'LDBDPdensity.o', 'LDDPdensity.o',
      'LDDPsurvival.o', 'LDPDdoublyintsba.o', 'LDTFPdensity.o',
      'LDTFPglmmpois.o', 'LDTFPsurvival.o', 'PSgamgam.o',
      'PSgamgauss.o', 'PSgamlogit.o', 'PSgampois.o', 'PSgamprob.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Authors@R field gives persons with no valid roles:
  Ben Marwick <bmarwick@uw.edu> [rev]
  Peter Slaughter <slaughter@nceas.ucsb.edu> [rev]
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   2.1Mb
File 'EBS/libs/i386/EBS.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'GeneralFunctions.o'
File 'EBS/libs/x64/EBS.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'GeneralFunctions.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
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 108-113 (parsing.Rmd) 
Error: processing vignette 'parsing.Rmd' failed with diagnostics:
argument is of length zero
Execution halted
Error in re-building vignettes:
  ...

Attaching package: 'scales'

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

    discard


Attaching package: 'gridExtra'

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

    combine


Attaching package: 'GGally'

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

    nasa

Quitting from lines 337-354 (exploring-election-data.Rmd) 
Error: processing vignette 'exploring-election-data.Rmd' failed with diagnostics:
could not find function "dmap"
Execution halted
File 'elrm/libs/i386/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'
File 'elrm/libs/x64/elrm.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'binomMCMC.o', 'functions.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'binomMCMC.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  7.3Mb
  sub-directories of 1Mb or more:
    xsd   5.4Mb
Missing or unexported object: 'xcms::profMat'
Packages in Depends field not imported from:
  'boot' 'xts' 'zoo'
  These packages need to be imported from (in the NAMESPACE file)
  for when this namespace is loaded but not attached.
Package required but not available: 'tidyquant'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FastRWeb.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Universidade Federal de Santa Maria <ppgcs@ufsm.br> [fnd]
Package required but not available: 'CVXR'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Warning: invalid input found on input connection 'fivethirtyeight-Ex.R'
Running examples in 'foghorn-Ex.R' failed
The error most likely occurred in:

> ### Name: cran_results
> ### Title: Table of the CRAN check results
> ### Aliases: cran_results
> 
> ### ** Examples
> 
>   if (curl::has_internet()) {
+     cran_results(pkg="MASS")
+   }
Error: Invalid package name(s): 'MASS'.
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > test_check("foghorn")
  -- 1. Error: check output for MASS (@test-foghorn.R#332)  ----------------------
  Invalid package name(s): 'MASS'.
  1: cran_results(pkg = "MASS") at testthat/test-foghorn.R:332
  2: cran_results_web(email, pkg, ...)
  3: read_cran_web_from_pkg(pkg, ...)
  4: stop("Invalid package name(s): ", paste(sQuote(pkg[bad]), collapse = ", "), ".", 
         call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 11 SKIPPED: 17 FAILED: 1
  1. Error: check output for MASS (@test-foghorn.R#332) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 23-25 (quick_start.Rmd) 
Error: processing vignette 'quick_start.Rmd' failed with diagnostics:
Invalid email address(es): 'francois.michonneau@gmail.com'.
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/FRESA.CAD.Rcheck/00install.out' for details.
installed size is  8.3Mb
  sub-directories of 1Mb or more:
    data   4.8Mb
    doc    1.6Mb
    libs   1.5Mb
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(FSelectorRcpp)
  > library(Matrix)
  > library(Rcpp)
  > library(RcppArmadillo)
  > library(dplyr)
  
  Attaching package: 'dplyr'
  
  The following object is masked from 'package:testthat':
  
      matches
  
  The following objects are masked from 'package:stats':
  
      filter, lag
  
  The following objects are masked from 'package:base':
  
      intersect, setdiff, setequal, union
  
  > library(entropy)
  
  Attaching package: 'entropy'
  
  The following object is masked from 'package:FSelectorRcpp':
  
      discretize
  
  > library(lintr)
  > 
  > test_check("FSelectorRcpp")
  -- 1. Failure: Catch unit tests pass (@test-cpp.R#5)  --------------------------
  C++ unit tests:
  ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
   is a Catch v1.9.6 host application.
  Run with -? for options
  
  -------------------------------------------------------------------------------
  Entropy tests | test-cpp.cpp
    Numeric entropy - comparsion with entropy package
  -------------------------------------------------------------------------------
  test-cpp.cpp:26
  ...............................................................................
  
  test-cpp.cpp:33: FAILED:
    CATCH_CHECK( entrR[0] == fselector::entropy::numeric_entropy(x.begin(), x.end()) )
  with expansion:
    1.0114042647 == 1.0114042647
  
  ===============================================================================
  test cases: 2 | 1 passed | 1 failed
  assertions: 5 | 4 passed | 1 failed
  
  
  == testthat results  ===========================================================
  OK: 89 SKIPPED: 0 FAILED: 1
  1. Failure: Catch unit tests pass (@test-cpp.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [20s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(fuzzyjoin)
  > 
  > test_check("fuzzyjoin")
  -- 1. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id1 not equal to c(1, 1, 2, 2, 3, 3).
  Lengths differ: 5 is not 6
  
  -- 2. Failure: Can do inner joins on intervals with findOverlaps arguments (@tes
  j_maxgap$id2 not equal to c(1, 2, 1, 2, 2, 3).
  Lengths differ: 5 is not 6
  
  == testthat results  ===========================================================
  OK: 224 SKIPPED: 0 FAILED: 2
  1. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#56) 
  2. Failure: Can do inner joins on intervals with findOverlaps arguments (@test_interval_join.R#57) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'GAMens-Ex.R' failed
The error most likely occurred in:

> ### Name: GAMens
> ### Title: Applies the GAMbag, GAMrsm or GAMens ensemble classifier to a
> ###   data set
> ### Aliases: GAMens
> ### Keywords: models classif
> 
> ### ** Examples
> 
> 
> ## Load data (mlbench library should be loaded)
> library(mlbench)
> data(Ionosphere)
> 
> ## Train a GAMens ensemble,
> ## estimated using 4 nonparametric terms and 2 linear terms
> Ionosphere.GAMens <- GAMens(Class~s(V3,4)+s(V4,4)+s(V5,3)+s(V6,5)+V7+V8,
+ Ionosphere ,3 , autoform=FALSE, iter=10 )
Error: could not find function "predict.gam"
Execution halted
installed size is 26.0Mb
  sub-directories of 1Mb or more:
    data  26.0Mb
Package required but not available: 'gge'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package required but not available: 'base2grob'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  Mark S.
        Handcock Developer <handcock@stat.ucla.edu>
  Michael S.
        Rendall Developer <mrendall@rand.org>
Authors@R field gives persons with no valid roles:
  Neal Richardson <neal.p.richardson@gmail.com> [rev] (Neal reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
  Julia Gustavsen <j.gustavsen@gmail.com> [rev] (Julia reviewed the package for ropensci, 
               see <https://github.com/ropensci/onboarding/issues/127>)
Running the tests in 'tests/bug1.R' failed.
Last 13 lines of output:
  'help.start()' for an HTML browser interface to help.
  Type 'q()' to quit R.
  
  > suppressMessages(library(gpclib))
  > to_numeric <- selectMethod(coerce, c("gpc.poly", "numeric"))
  > load("bug1_data.RData")
  > plot(p)  ## loads a polygon, looks fine
  > plot(as(vec, "gpc.poly"))  ## looks fine
  > clip <- to_numeric(p); str(clip)
   num [1:17] 1 7 0 570545 7890092 ...
  > 
  > ## Crashes R 2.14 and 2.15 (32-bit) on Windows
  > vec <- .Call("Rgpc_polygon_clip", vec, clip, 3, PACKAGE="gpclib")
Invalid citation information in 'inst/CITATION':
  Error in .citation(rval): attempt to set an attribute on NULL
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/gpuR.Rcheck/00install.out' for details.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R   5.4Mb
Package required but not available: 'hexSticker'

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Package suggested but not available for checking: 'trackr'
Package required and available but unsuitable version: 'VGAM'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  The R Consortium [fnd]
installed size is  5.6Mb
  sub-directories of 1Mb or more:
    doc    2.5Mb
    libs   1.5Mb
File 'hSDM/libs/i386/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'
File 'hSDM/libs/x64/hSDM.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'useful.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'hSDM.Nmixture.o', 'hSDM.Nmixture.iCAR.o', 'hSDM.ZIB.o',
      'hSDM.ZIB.iCAR.alteration.o', 'hSDM.ZIB.iCAR.o', 'hSDM.ZIP.o',
      'hSDM.ZIP.iCAR.alteration.o', 'hSDM.ZIP.iCAR.o',
      'hSDM.binomial.o', 'hSDM.binomial.iCAR.o', 'hSDM.poisson.o',
      'hSDM.poisson.iCAR.o', 'hSDM.siteocc.o', 'hSDM.siteocc.iCAR.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(hyphenatr)
  > 
  > test_check("hyphenatr")
  -- 1. Failure: we can do something (@test-hyphenatr.R#16)  ---------------------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "tÃ¤=gelÃ®ch"
  y[1]: "tä=gelîch"
  
  == testthat results  ===========================================================
  OK: 4 SKIPPED: 0 FAILED: 1
  1. Failure: we can do something (@test-hyphenatr.R#16) 
  
  Error: testthat unit tests failed
  Execution halted
Dscores: no visible global function definition for 'filter'
Dscores: no visible global function definition for 'sd'
Gscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'filter'
MiniDscores: no visible global function definition for 'object.size'
RobustScores: no visible global function definition for 'filter'
SplitHalf: no visible global function definition for 'cor'
TestRetest: no visible global function definition for 'filter'
TestRetest: no visible global function definition for 'cor'
WPRscores: no visible global function definition for 'filter'
WPRscores: no visible global function definition for 'quantile'
WPRscores: no visible global function definition for 'sd'
computeMinid: no visible global function definition for 'sd'
doP1P2: no visible global function definition for 'filter'
doP1P2: no visible global function definition for 'sd'
doP1P2P3P4: no visible global function definition for 'filter'
specialvar: no visible global function definition for 'var'
Undefined global functions or variables:
  cor filter object.size quantile sd var
Consider adding
  importFrom("stats", "cor", "filter", "quantile", "sd", "var")
  importFrom("utils", "object.size")
to your NAMESPACE file.
installed size is  9.3Mb
  sub-directories of 1Mb or more:
    R      1.4Mb
    data   1.3Mb
    doc    3.2Mb
    libs   2.9Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         val
     })(Assessment.StockCode = "cod.27.47d20", Assessment.AssessmentYear = 2015L, Assessment.ContactPerson = "colin.millar@ices.dk", 
         Assessment.NameSystemProducedFile = "icesSAG R package version 1.3.2", Assessment.Fish_Data.Year = 2000L, 
         Assessment.Fish_Data.Year = 2001L, Assessment.Fish_Data.Year = 2002L, Assessment.Fish_Data.Year = 2003L, 
         Assessment.Fish_Data.Year = 2004L, Assessment.Fish_Data.Year = 2005L, Assessment.Fish_Data.Year = 2006L, 
         Assessment.Fish_Data.Year = 2007L, Assessment.Fish_Data.Year = 2008L, Assessment.Fish_Data.Year = 2009L, 
         Assessment.Fish_Data.Year = 2010L, Assessment.Fish_Data.Year = 2011L, Assessment.Fish_Data.Year = 2012L, 
         Assessment.Fish_Data.Year = 2013L, Assessment.Fish_Data.Year = 2014L, Assessment.Fish_Data.Year = 2015L)
  
  == testthat results  ===========================================================
  OK: 1334 SKIPPED: 0 FAILED: 1
  1. Error: SAG upload (@test-test.R#13) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Andee Kaplan [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
  Carl Ganz [rev] (Reviewer for rOpensci review process https://github.com/ropensci/onboarding/issues/107)
Error in re-building vignettes:
  ...
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  invalid input found on input connection 'D:\temp\RtmpqwXtIK\ex_data1297019d7404.csv2'
Warning in read.table(file = file, header = header, sep = sep, quote = quote,  :
  incomplete final line found by readTableHeader on 'D:\temp\RtmpqwXtIK\ex_data1297019d7404.csv2'
Quitting from lines 31-32 (incadoc.Rmd) 
Error: processing vignette 'incadoc.Rmd' failed with diagnostics:
cannot open URL 'http://www.cancercentrum.se/globalassets/cancerdiagnoser/lunga-och-lungsack/dokument/styrdokument.pdf'
Execution halted
Package required and available but unsuitable version: 'libcoin'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Namespace with empty importFrom: 'miscTools'
Running 'testthat.R' [12s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(jmv)
  
  Attaching package: 'jmv'
  
  The following object is masked from 'package:stats':
  
      anova
  
  > 
  > test_check("jmv")
  -- 1. Error: anovarm works (@testanovarm.R#37)  --------------------------------
  subscript out of bounds
  1: jmv::anovaRM(data = data, rm = rm, rmCells = rmCells, bs = "between", rmTerms = list("intake"), 
         bsTerms = list("between"), postHoc = postHoc) at testthat/testanovarm.R:37
  2: analysis$run()
  3: try({
         result <- private$.run()
     }, silent = TRUE)
  4: eval(expr)
  5: private$.run()
  6: private$.populateEffectsTables(result)
  
  == testthat results  ===========================================================
  OK: 82 SKIPPED: 2 FAILED: 1
  1. Error: anovarm works (@testanovarm.R#37) 
  
  Error: testthat unit tests failed
  Execution halted
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant number: MR/M013227/1)
Authors@R field gives persons with no valid roles:
  Medical Research Council [fnd] (Grant numbers: G0400615 and MR/M013227/1)
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(jpndistrict)
  Loading required package: jpmesh
  This package provide map data is based on the Digital Map 25000(Map
  Image) published by Geospatial Information Authorityof Japan (Approval
  No.603FY2017 information usage <http://www.gsi.go.jp>)
  > 
  > test_check("jpndistrict")
  -- 1. Failure: jpn_pref (@test-spdf_jpn.R#20)  ---------------------------------
  Names of `df_pref2` ('jis_code', 'prefecture', 'geometry') don't match 'jis_code', 'prefecture', '.'
  
  == testthat results  ===========================================================
  OK: 41 SKIPPED: 0 FAILED: 1
  1. Failure: jpn_pref (@test-spdf_jpn.R#20) 
  
  Error: testthat unit tests failed
  Execution halted
StartKappa: no visible global function definition for 'read.csv'
StartKappa: no visible global function definition for 'na.omit'
StartKappa: no visible global function definition for 'write.csv2'
Undefined global functions or variables:
  na.omit read.csv write.csv2
Consider adding
  importFrom("stats", "na.omit")
  importFrom("utils", "read.csv", "write.csv2")
to your NAMESPACE file.
Running examples in 'ks-Ex.R' failed
The error most likely occurred in:

> ### Name: Hpi
> ### Title: Plug-in bandwidth selector
> ### Aliases: Hpi Hpi.diag hpi
> ### Keywords: smooth
> 
> ### ** Examples
> 
> data(unicef)
> Hpi(unicef, pilot="dscalar")
Note: method with signature 'ANY#sparseMatrix' chosen for function 'kronecker',
 target signature 'dgeMatrix#dtTMatrix'.
 "Matrix#ANY" would also be valid
Error in norm(Matrix(psi2r8.ns, nrow = 1) %*% (Matrix(vec(diag(d)), ncol = 1) %*%  : 
  argument type[1]='2' must be one of 'M','1','O','I','F' or 'E'
Calls: Hpi -> gdscalar -> norm -> norm
Execution halted
Authors@R field gives persons with no valid roles:
  Laura Graham [rev] (Laura reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
  Jeffrey Hollister [rev] (Jeffrey reviewed the package for rOpenSci, see 
                  https://github.com/ropensci/onboarding/issues/188)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/languageserver.Rcheck/00install.out' for details.
File 'leaps/libs/i386/leaps.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'leaps.o'
File 'leaps/libs/x64/leaps.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'leaps.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    libs   4.6Mb
Running examples in 'lmem.gwaser-Ex.R' failed
The error most likely occurred in:

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

    No. individuals:    179 

    No. phenotypes:     3 
    Percent phenotyped: 100 100 100 

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

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [26s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 3, minute = 36, second = 5, dt = structure(1522719371.22966, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2429 SKIPPED: 4 FAILED: 6
  1. Error: Comparison operators work with POSIX and Date objects (@test-ops-compare.R#4) 
  2. Error: difftime comparison with periods works (@test-ops-compare.R#63) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  4. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  5. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  6. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [28s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 3, minute = 36, second = 5, dt = structure(1522719400.41708, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 2442 SKIPPED: 4 FAILED: 4
  1. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#82) 
  2. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#83) 
  3. Failure: with_tz throws warning on unrecognized time zones (@test-timezones.R#84) 
  4. Error: Updateing on seconds doesn't affect hours (@test-update.R#414) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "£12.00"
  
  -- 2. Failure: Complex amounts can be converted (@test_conversion.R#8)  --------
  `x` not equal to `expected`.
  1/1 mismatches
  x[1]: "Â£12,000.00"
  y[1]: "£12,000.00"
  
  == testthat results  ===========================================================
  OK: 6 SKIPPED: 0 FAILED: 2
  1. Failure: Simple amounts can be converted (@test_conversion.R#4) 
  2. Failure: Complex amounts can be converted (@test_conversion.R#8) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  9: (function (...) 
     .subset2(public_bind_env, "finalize")())(<environment>)
  10: .subset2(public_bind_env, "finalize")()
  11: is_open(self$con)
  12: isOpen(con)
  
  Error in signalCondition(e) : 
    no function to return from, jumping to top level
  Calls: <Anonymous> ... isOpen -> .handleSimpleError -> h -> signalCondition
  testthat results ================================================================
  OK: 22 SKIPPED: 0 FAILED: 1
  1. Error: The pipe function (@test_nse.R#23) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'MANOVA.RM-Ex.R' failed
The error most likely occurred in:

> ### Name: MANOVA.wide
> ### Title: Tests for Multivariate Data in Semi-Parametric Factorial Designs
> ### Aliases: MANOVA.wide
> 
> ### ** Examples
> 
> #Example on producing plastic film from Krzanowski (1998, p. 381), see \code{manova.summary}
> tear <- c(6.5, 6.2, 5.8, 6.5, 6.5, 6.9, 7.2, 6.9, 6.1, 6.3,
+           6.7, 6.6, 7.2, 7.1, 6.8, 7.1, 7.0, 7.2, 7.5, 7.6)
> gloss <- c(9.5, 9.9, 9.6, 9.6, 9.2, 9.1, 10.0, 9.9, 9.5, 9.4,
+            9.1, 9.3, 8.3, 8.4, 8.5, 9.2, 8.8, 9.7, 10.1, 9.2)
> opacity <- c(4.4, 6.4, 3.0, 4.1, 0.8, 5.7, 2.0, 3.9, 1.9, 5.7,
+              2.8, 4.1, 3.8, 1.6, 3.4, 8.4, 5.2, 6.9, 2.7, 1.9)
> rate     <- gl(2,10, labels = c("Low", "High"))
> additive <- gl(2, 5, length = 20, labels = c("Low", "High"))
> example <- data.frame(tear, gloss, opacity, rate, additive)
> fit <- MANOVA.wide(cbind(tear, gloss, opacity) ~ rate * additive, 
+ data = example, iter = 100, CPU = 1)
Error in deparse(...) : unused argument (lex.order = TRUE)
Calls: MANOVA.wide ... split.default -> .NotYetUsed -> gettextf -> sprintf -> deparse
Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 162-174 (Introduction_to_MANOVA.RM.Rmd) 
Error: processing vignette 'Introduction_to_MANOVA.RM.Rmd' failed with diagnostics:
unused argument (lex.order = TRUE)
Execution halted
Running 'testthat.R' [19s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
  6: row_ievora(x = x, g = grp)
  7: row_t_welch(x[, g == 1, drop = FALSE], x[, g == 0, drop = FALSE])
  8: rowSums((x - mxs)^2, na.rm = TRUE)
  9: stop("'x' must be an array of at least two dimensions")
  
  == testthat results  ===========================================================
  OK: 820 SKIPPED: 0 FAILED: 4
  1. Error: x and y can have 0 rows and 0 columns (@test-parameters-special-cases.R#48) 
  2. Error: groups can all be NA (@test-parameters-special-cases.R#103) 
  3. Error: groups can all be NaN (@test-parameters-special-cases.R#113) 
  4. Error: all observations can be in the same group (@test-parameters-special-cases.R#127) 
  
  Error: testthat unit tests failed
  Execution halted
File 'maxent/libs/i386/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'
File 'maxent/libs/x64/maxent.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'sgd.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.3Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.2Mb
-- Attaching packages --------------------------------------- tidyverse 1.2.1 --
v ggplot2 2.2.1     v purrr   0.2.4
v tibble  1.4.2     v dplyr   0.7.4
v tidyr   0.8.0     v stringr 1.3.0
v readr   1.1.1     v forcats 0.3.0
-- Conflicts ------------------------------------------ tidyverse_conflicts() --
x dplyr::filter() masks stats::filter()
x dplyr::lag()    masks stats::lag()
Loading required package: lattice
Error in unloadNamespace(package) : 
  namespace 'lattice' is imported by 'nlme', 'Matrix', 'psych', 'mosaic' so cannot be unloaded
Error : .onAttach failed in attachNamespace() for 'mdsr', details:
  call: library(pkg, character.only = TRUE, logical.return = TRUE, lib.loc = lib.loc, 
  error: Package 'lattice' version 0.20.35 cannot be unloaded
Error: package or namespace load failed for 'mdsr'
Execution halted

It looks like this package has a loading problem when not on .libPaths:
see the messages for details.
installed size is  8.0Mb
  sub-directories of 1Mb or more:
    doc    1.0Mb
    libs   3.8Mb
    misc   1.1Mb
File 'MigClim/libs/i386/MigClim.dll':
  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'
File 'MigClim/libs/x64/MigClim.dll':
  Found 'rand', possibly from 'rand' (C)
    Objects: 'genclust.o', 'migrate.o', 'src_cell.o', 'validate.o'
  Found 'srand', possibly from 'srand' (C)
    Objects: 'genclust.o', 'migrate.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Missing or unexported object: 'tools::CRAN_package_db'
Package required and available but unsuitable version: 'S4Vectors'

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

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/monoreg.Rcheck/00install.out' for details.
File 'MRwarping/libs/i386/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'
File 'MRwarping/libs/x64/MRwarping.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'interfaceRC_warp.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Authors@R field gives persons with no valid roles:
  YouGov [fnd]
Running 'testthat.R' [30s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = 3, wday = integer(0), 
         hour = 4, minute = 10, second = 42.2364139556885, dt = structure(1522721440.23641, class = c("POSIXct", 
         "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 67 SKIPPED: 0 FAILED: 3
  1. Error: character date handling: yyyy-mm-dd hh:mm:ss in past (@test-naptime.R#126) 
  2. Error: character date handling: yyyy-mm-dd hh:mm:ss in future (@test-naptime.R#136) 
  3. Error: Invalid Period throws error (@test-naptime.R#168) 
  
  Error: testthat unit tests failed
  Execution halted
File 'NeatMap/libs/i386/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'
File 'NeatMap/libs/x64/NeatMap.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'nMDS_R.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'nMDS_R.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
File 'NetSim/libs/i386/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'
File 'NetSim/libs/x64/NetSim.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'utils/Random.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'utils/Random.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is 15.9Mb
  sub-directories of 1Mb or more:
    CppCode   2.5Mb
    R         3.3Mb
    include   5.7Mb
    libs      1.8Mb
    tests     1.3Mb
installed size is  8.5Mb
  sub-directories of 1Mb or more:
    data      4.3Mb
    reports   2.2Mb
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    data   6.9Mb
Authors@R field gives persons with no valid roles:
  Julia Silge [rev] (Julia Silge reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/36.)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/OpenCL.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMPController.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OpenMx.Rcheck/00install.out' for details.
Running 'testthat.R' [32s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [33s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  5: sapply(1:nSheets, function(i) isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]])))
  6: lapply(X = X, FUN = FUN, ...)
  7: FUN(X[[i]], ...)
  8: isTRUE(all.equal(x$colWidths[[i]], y$colWidths[[i]]))
  9: all.equal(x$colWidths[[i]], y$colWidths[[i]])
  10: all.equal.list(x$colWidths[[i]], y$colWidths[[i]])
  11: attr.all.equal(target, current, ...)
  12: mode(current)
  
  == testthat results  ===========================================================
  OK: 505 SKIPPED: 2 FAILED: 1
  1. Error: loadWorkbook from different sources (@test-read_sources.R#49) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/OptimClassifier.Rcheck/00install.out' for details.
Package required but not available: 'CVXR'

Package suggested but not available for checking: 'Rmosek'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [10s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 556 SKIPPED: 0 FAILED: 2
  1. Error: interval: year (@test_thicken_integration.R#7) 
  2. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
         week_start = 7L) 
     {
         .Call(`_lubridate_C_update_dt`, dt, year, month, yday, mday, wday, hour, minute, 
             second, tz, roll, week_start)
     })(year = integer(0), month = integer(0), yday = integer(0), mday = c(7, 7, 9, 10
     ), wday = integer(0), hour = c(9, 9, 13, 10), minute = c(11, 46, 25, 45), second = c(21, 
     48, 17, 11), dt = structure(c(1467875481, 1467877608, 1470741917, 1473497111), class = c("POSIXct", 
     "POSIXt"), tzone = ""), roll = FALSE, tz = "", week_start = 7)
  
  == testthat results  ===========================================================
  OK: 572 SKIPPED: 0 FAILED: 1
  1. Error: interval: month (@test_thicken_integration.R#67) 
  
  Error: testthat unit tests failed
  Execution halted
Packages required and available but unsuitable versions: 'libcoin' 'inum'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  Loading required package: pathological
  -- 1. Failure: standardize_path works with missing files with ./ prefix (@test_s
  standardize_path(x) not equal to `expected`.
  1/2 mismatches
  x[1]: "D:/RCompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  x[1]: ompose_path.R"
  y[1]: "D:/Rcompile/CRANpkg/local/3.3/pathological.Rcheck/tests/testthat/test_dec
  y[1]: ompose_path.R"
  
  == testthat results  ===========================================================
  OK: 187 SKIPPED: 18 FAILED: 1
  1. Failure: standardize_path works with missing files with ./ prefix (@test_standardize_path.R#198) 
  
  Error: testthat unit tests failed
  Execution halted
installed size is  8.9Mb
  sub-directories of 1Mb or more:
    R      2.4Mb
    data   2.1Mb
    libs   2.3Mb
Running 'testthat.R' [13s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1. Error: (unknown) (@test_GTE-summary_by.R#7) 
  2. Error: all queries match expected values (@test_GTE_paper_count.R#132) 
  3. Error: document type = *journal-paper* matches (@test_document_type.R#11) 
  4. Error: document type = *conference-paper* matches (@test_document_type.R#22) 
  5. Error: make_search_url matches number of papers from_year to_year (@test_from_year_to_year.R#12) 
  6. Error: is_dctype_enabled = FALSE (@test_is_dctype_enabled.R#8) 
  7. Error: is_dctype_enabled = TRUE (@test_is_dctype_enabled.R#21) 
  8. Error: both dataframes return rows - test #5 (@test_joining.R#11) 
  9. Error: both dataframes return rows - test #3 (@test_joining.R#25) 
  1. ...
  
  Error: testthat unit tests failed
  In addition: Warning message:
  closing unused connection 5 (https://www.onepetro.org/search?q=smartwell&peer_reviewed=&published_between=&from_year=&to_year=) 
  Execution halted
Package required and available but unsuitable version: 'qusage'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
File 'PhaseType/libs/i386/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'
File 'PhaseType/libs/x64/PhaseType.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'LJMA_arms.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
pointdensity: no visible global function definition for
  'txtProgressBar'
pointdensity: no visible global function definition for
  'setTxtProgressBar'
pointdensity: no visible global function definition for 'flush.console'
Undefined global functions or variables:
  flush.console setTxtProgressBar txtProgressBar
Consider adding
  importFrom("utils", "flush.console", "setTxtProgressBar",
             "txtProgressBar")
to your NAMESPACE file.
Packages which this enhances but not available for checking:
  'org.Ag.eg.db' 'org.Pt.eg.db' 'org.Ss.eg.db' 'org.Bt.eg.db'
  'org.Ce.eg.db' 'org.Cf.eg.db' 'org.Dr.eg.db' 'org.EcK12.eg.db'
  'org.EcSakai.eg.db' 'org.Gg.eg.db' 'org.Mmu.eg.db' 'org.Pf.plasmo.db'
  'org.Xl.eg.db'
Running 'testthat.R' [135s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  ..
  ..
  == testthat results  ===========================================================
  OK: 8417 SKIPPED: 53 FAILED: 8
  1. Error: compile (@test_add_connected_constraints.R#12) 
  2. Error: (unknown) (@test_add_connected_constraints.R#3) 
  3. Error: compile (@test_add_connected_constraints.R#12) 
  4. Error: (unknown) (@test_add_connected_constraints.R#3) 
  5. Error: compile (@test_add_connected_constraints.R#12) 
  6. Error: (unknown) (@test_add_connected_constraints.R#3) 
  7. Error: compile (@test_add_connected_constraints.R#12) 
  8. Error: (unknown) (@test_add_connected_constraints.R#3) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'run-all.R' [25s]
Running the tests in 'tests/run-all.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("ProjectTemplate")
  Loading required package: ProjectTemplate
  Read 1 item
  v | OK F W S | Context
  
  - |  1       | 0
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  v | OK F W S | Context
  
  - |  1       | 0
  == Results =====================================================================
  OK:       1
  Failed:   0
  Warnings: 0
  Skipped:  0
  -- 1. Failure: ignored data files are not loaded (@test-load.R#183)  -----------
  `load.project(override.config = list(data_ignore = ""))` threw an error with unexpected message.
  Expected match: "file is encrypted or is not a database"
  Actual message: "file is not a database"
  
  WARNING: Perl module Compress::Raw::Zlib cannot be loaded.
  WARNING: Perl module Spreadsheet::ParseXLSX cannot be loaded.
  WARNING: Microsoft Excel 2007 'XLSX' formatted files will not be processed.
  == testthat results  ===========================================================
  OK: 637 SKIPPED: 4 FAILED: 1
  1. Failure: ignored data files are not loaded (@test-load.R#183) 
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'psychmeta-Ex.R' failed
The error most likely occurred in:

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

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

d Values Corrected for Measurement Error:
---------------------------------------------------------------------------------------
  value CI_LL_95 CI_UL_95   n n_effective
1 0.595      0.3    0.912 300         183
> 
> ## Correction for direct range restriction in the continuous variable
> correct_d(correction = "uvdrr_y", d = .5, ryy = .8, uy = .7,
+           rGg = .9, pi = .7, pa = .5)
Error in indirect_rr | rxxa_consistency : 
  operations are possible only for numeric, logical or complex types
Calls: correct_d -> correct_r -> correct_r_uvdrr
Execution halted
Authors@R field gives persons with no valid roles:
  Sasha Epskamp [rev] (Sasha reviewed the package for JOSS, see https://github.com/openjournals/joss-reviews/issues/470)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    R     1.3Mb
    doc   2.4Mb
Error in re-building vignettes:
  ...
downloaded 0 bytes

Quitting from lines 34-38 (iGWAS-DataExample.Rmd) 
Error: processing vignette 'iGWAS-DataExample.Rmd' failed with diagnostics:
cannot download all files
Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/qtbase.Rcheck/00install.out' for details.
installed size is 10.2Mb
  sub-directories of 1Mb or more:
    R         1.4Mb
    contrib   3.6Mb
    doc       2.9Mb
Running 'tests.R' [1s]
Running the tests in 'tests/tests.R' failed.
Last 13 lines of output:
  > op.warn <- getOption("warn")
  > options(warn = 2)
  > quantmod::getSymbols("SPY", src = "google", from = Sys.Date() - 10)
  'getSymbols' currently uses auto.assign=TRUE by default, but will
  use auto.assign=FALSE in 0.5-0. You will still be able to use
  'loadSymbols' to automatically load data. getOption("getSymbols.env")
  and getOption("getSymbols.auto.assign") will still be checked for
  alternate defaults.
  
  This message is shown once per session and may be disabled by setting 
  options("getSymbols.warning4.0"=FALSE). See ?getSymbols for details.
  Error in download.file(paste(google.URL, "q=", Symbols.name, "&startdate=",  : 
    (converted from warning) cannot open URL 'http://finance.google.com/finance/historical?q=SPY&startdate=Mar+24,+2018&enddate=Apr+03,+2018&output=csv': HTTP status was '403 Forbidden'
  Calls: <Anonymous> -> do.call -> getSymbols.google -> download.file
  Execution halted
File 'qVarSel/libs/i386/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'
File 'qVarSel/libs/x64/qVarSel.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'qVarSelH.o'
  Found 'srand', possibly from 'srand' (C)
    Object: 'qVarSelH.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    R      2.0Mb
    libs   1.8Mb
Found the following significant warnings:
  Warning: replacing previous import 'Rcmdr::Confint' by 'car::Confint' when loading 'RcmdrPlugin.BCA'
See 'd:/Rcompile/CRANpkg/local/3.3/RcmdrPlugin.BCA.Rcheck/00install.out' for details.
Found the following significant warnings:
  Warning: replacing previous import 'car::Confint' by 'Rcmdr::Confint' when loading 'RcmdrPlugin.UCA'
See 'd:/Rcompile/CRANpkg/local/3.3/RcmdrPlugin.UCA.Rcheck/00install.out' for details.
installed size is  6.2Mb
  sub-directories of 1Mb or more:
    doc   2.7Mb
    po    2.1Mb
Running 'testthat.R' [82s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  > library(testthat)
  > library(rcongresso)
  > 
  > test_check("rcongresso")
  -- 1. Failure: Dimensoes do dataframe (@test_votacoes.R#54)  -------------------
  dim(votos_pec241) not equal to c(478, 10).
  1/2 mismatches
  [1] 500 - 478 == 22
  
  == testthat results  ===========================================================
  OK: 66 SKIPPED: 0 FAILED: 1
  1. Failure: Dimensoes do dataframe (@test_votacoes.R#54) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rcplex.Rcheck/00install.out' for details.
installed size is  8.6Mb
  sub-directories of 1Mb or more:
    include   1.7Mb
    lib       3.9Mb
    libs      2.9Mb
Missing or unexported object: 'tools::package_native_routine_registration_skeleton'
Running examples in 'RCzechia-Ex.R' failed
The error most likely occurred in:

> ### Name: kraje
> ### Title: Regions (kraje) of the Czech Republic
> ### Aliases: kraje
> 
> ### ** Examples
> 
> library(sf)
Linking to GEOS 3.6.1, GDAL 2.2.3, proj.4 4.9.3
> 
> hranice <- kraje()
Error: unknown input format
Execution halted
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > 
  > test_check("RCzechia")
  Loading required package: RCzechia
  -- 1. Error: (unknown) (@test-jla.R#6)  ----------------------------------------
  unknown input format
  1: expect_that(is.data.frame(republika()), is_true()) at testthat/test-jla.R:6
  2: condition(object)
  3: expect_true(x)
  4: quasi_label(enquo(object), label)
  5: eval_bare(get_expr(quo), get_env(quo))
  6: is.data.frame(republika())
  7: republika()
  8: readRDS(url(remote_df))
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-jla.R#6) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RDieHarder.Rcheck/00install.out' for details.
Running 'testthat.R' [11s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  `encoding(rt, verbose = TRUE)` produced unexpected messages.
  Expected match: Probable encoding: UTF-8
  Actual values:
  * Probable encoding: ISO-8859-2
  * 
  
  
  == testthat results  ===========================================================
  OK: 127 SKIPPED: 11 FAILED: 3
  1. Failure: test encoding function on simple text files (@test-encoding.R#7) 
  2. Failure: test encoding function on simple text files (@test-encoding.R#12) 
  3. Failure: test encoding function on simple text files (@test-encoding.R#17) 
  
  Error: testthat unit tests failed
  Execution halted
Package suggested but not available for checking: 'rsolr'
Package required and available but unsuitable version: 'stats'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  gdkFuncs.c:1466:31: warning: passing argument 1 of 'gdk_drag_get_protocol' makes pointer from integer without a cast
  gdkFuncs.c:1510:52: warning: passing argument 2 of 'gdk_drag_get_protocol_for_display' makes pointer from integer without a cast
See 'd:/Rcompile/CRANpkg/local/3.3/RGtk2.Rcheck/00install.out' for details.
installed size is 18.6Mb
  sub-directories of 1Mb or more:
    R      1.8Mb
    help  10.6Mb
    libs   4.7Mb
.install_system_dependencies : <anonymous>: no visible global function
  definition for 'unzip'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'menu'
.install_system_dependencies : install_system_dep: no visible global
  function definition for 'download.file'
as.GParamSpec: no visible global function definition for 'new'
Undefined global functions or variables:
  download.file menu new unzip
Consider adding
  importFrom("methods", "new")
  importFrom("utils", "download.file", "menu", "unzip")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Non-portable flags in variable 'PKG_CPPFLAGS':
  -g
File 'RInside/libs/i386/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/RInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/x64/libRInside.dll':
  Found 'srand', possibly from 'srand' (C)
    Object: 'RInside.o'
File 'RInside/libs/i386/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/RInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/i386/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'
File 'RInside/libs/x64/libRInside.dll':
  Found non-API calls to R: 'R_CleanTempDir', 'R_DefParams',
    'R_ReplDLLdo1', 'R_ReplDLLinit', 'R_RunExitFinalizers',
    'R_SetParams', 'R_TempDir', 'Rf_endEmbeddedR', 'Rf_initEmbeddedR',
    'getRUser', 'get_R_HOME'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Packages required and available but unsuitable versions: 'grid' 'utils'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Found the following significant warnings:
  jri.h:21:20: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri.c:308:27: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  jri_glue.c:24:15: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/rJava.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/i386/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'd:/Rcompile/CRANpkg/lib/3.3/rJava/libs/x64/rJava.dll':
  Found 'abort', possibly from 'abort' (C), 'runtime' (Fortran)
File 'rJava/libs/i386/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'
File 'rJava/libs/x64/rJava.dll':
  Found non-API call to R: 'R_GlobalContext'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    rmd   5.9Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rmetasim.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/Rmosek.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/Rmpfr.Rcheck/00install.out' for details.
installed size is 10.0Mb
  sub-directories of 1Mb or more:
    R   9.9Mb
Authors@R field gives persons with no valid roles:
  Andrew MacDonald [rev] (Andrew MacDonald reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
  Andy  Teucher [rev] (Andy Teucher reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/24)
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/ROracle.Rcheck/00install.out' for details.
Authors@R field gives persons with no valid roles:
  Scott Chamberlain [rev] (0000-0003-1444-9135)
installed size is  5.2Mb
  sub-directories of 1Mb or more:
    extdata   1.0Mb
    libs      2.8Mb
Running 'test-all.R' [29s]
Running the tests in 'tests/test-all.R' failed.
Last 13 lines of output:
  7: jsonlite::fromJSON(paste(get_base_url(), "tnrs/gnr/resolve?names=", taxa.string, 
         sep = ""))
  8: fromJSON_string(txt = txt, simplifyVector = simplifyVector, simplifyDataFrame = simplifyDataFrame, 
         simplifyMatrix = simplifyMatrix, flatten = flatten, ...)
  9: parseJSON(txt, bigint_as_char)
  10: parse_con(txt, bigint_as_char)
  11: open(con, "rb")
  12: open.connection(con, "rb")
  
  == testthat results  ===========================================================
  OK: 36 SKIPPED: 0 FAILED: 1
  1. Error: Resolving names with GNR works (@test_resolver.R#5) 
  
  Error: testthat unit tests failed
  Execution halted
Warning in self$configPolyhedraSource(source.config = sources.config[[source]],  :
  bytecode version mismatch; using eval

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

Probably some imports need to be declared in the NAMESPACE file.
Found the following significant warnings:
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/RCompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:824:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomdefaultlatentmodel.hpp:842:13: warning: this decimal constant is unsigned only in ISO C90
  d:/Rcompile/CRANpkg/extralibs330/quantlib/ql/experimental/credit/randomlosslatentmodel.hpp:84:13: warning: this decimal constant is unsigned only in ISO C90
See 'd:/Rcompile/CRANpkg/local/3.3/RQuantLib.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/RSAP.Rcheck/00install.out' for details.
Found the following significant warnings:
   #warning Please include winsock2.h before windows.h
  qap_decode.c:200:41: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:200:54: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:34: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:238:55: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:39: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
  qap_decode.c:244:60: warning: cast from pointer to integer of different size [-Wpointer-to-int-cast]
See 'd:/Rcompile/CRANpkg/local/3.3/Rserve.Rcheck/00install.out' for details.
Note: information on .o files for i386 is not available
Note: information on .o files for x64 is not available


See 'Writing portable packages' in the 'Writing R Extensions' manual.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsolr.Rcheck/00install.out' for details.
Running 'testthat.R' [282s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RStoolbox) 
  > 
  > 
  > Sys.setenv("R_TESTS" = "") ## needed to pass R CMD check: https://github.com/hadley/testthat/issues/144
  > 
  > test_check("RStoolbox")
  -- 1. Error: classification, without class mapping (@test-validateMap.R#19)  ---
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "classNum", classMapping = NULL) at testthat/test-validateMap.R:19
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Running 'testthat.R' [317s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(RStoolbox) 
  > 
  > 
  > Sys.setenv("R_TESTS" = "") ## needed to pass R CMD check: https://github.com/hadley/testthat/issues/144
  > 
  > test_check("RStoolbox")
  -- 1. Error: classification, without class mapping (@test-validateMap.R#19)  ---
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "classNum", classMapping = NULL) at testthat/test-validateMap.R:19
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  -- 2. Error: classification, with class mapping (@test-validateMap.R#26)  ------
  `data` and `reference` should be factors with the same levels.
  1: validateMap(sc$map, valData = poly, nSample = 100, responseCol = "class", classMapping = sc$classMapping) at testthat/test-validateMap.R:26
  2: confusionMatrix(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, "reference"])
  3: confusionMatrix.default(valiSet[[1]][, "prediction"], reference = valiSet[[1]][, 
         "reference"])
  4: stop("`data` and `reference` should be factors with the same levels.", call. = FALSE)
  
  == testthat results  ===========================================================
  OK: 925 SKIPPED: 2 FAILED: 2
  1. Error: classification, without class mapping (@test-validateMap.R#19) 
  2. Error: classification, with class mapping (@test-validateMap.R#26) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/rsunlight.Rcheck/00install.out' for details.
getSVGToolTipMode: no visible global function definition for 'dev.cur'
setSVGShapeContents: no visible global function definition for
  'dev.cur'
setSVGShapeToolTip: no visible global function definition for 'dev.cur'
setSVGShapeURL: no visible global function definition for 'dev.cur'
Undefined global functions or variables:
  dev.cur
Consider adding
  importFrom("grDevices", "dev.cur")
to your NAMESPACE file.
Running examples in 'RSVGTipsDevice-Ex.R' failed
The error most likely occurred in:

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

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

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

other attached packages:
[1] RSVGTipsDevice_1.0-4
> devSVGTips("svgplot1.svg", toolTipMode=1,
+     title="SVG example plot 1: shapes and points, tooltips are title + 1 line")
> plot(c(0,10),c(0,10), type="n", xlab="x", ylab="y",
+     main="Example SVG plot with title + 1 line tips (mode=1)")
> setSVGShapeToolTip(title="A rectangle", desc="that is yellow")
> rect(1,1,4,6, col='yellow')
> setSVGShapeToolTip(title="1st circle with title only")
> points(5.5,7.5,cex=20,pch=19,col='red')
> setSVGShapeToolTip(title="A triangle", desc="big and green")
> polygon(c(3,6,8), c(3,6,3), col='green')
> # no tooltips on these points
> points(2:8, 8:2, cex=3, pch=19, col='black')
> # tooltips on each these points
> invisible(sapply(1:7, function(x)
+ {setSVGShapeToolTip(title=paste("point", x))
+  points(x+1, 8-x, cex=3, pch=1, col='black')}))
> setSVGShapeToolTip(title="Text", desc="can have a tool tip too!")
> text(x=4, y=9, lab="Poke me!", col="blue")
> dev.off()
Authors@R field gives persons with no valid roles:
  ERC Grant Agreement number 336167 - the CHAI Project [fnd]
  Lucy D'Agostino McGowan [rev] (Lucy D'Agostino McGowan reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
  Kara  Woo [rev] (Kara Woo reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/126)
Package required and available but unsuitable version: 'RGtk2'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
installed size is  5.1Mb
  sub-directories of 1Mb or more:
    sample_data   3.0Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/s2.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/ScottKnottESD.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/selectiveInference.Rcheck/00install.out' for details.
Running 'testthat.R' [9s]
Running the tests in 'tests/testthat.R' failed.
Complete output:
  > library(testthat)
  > library(SentimentAnalysis)
  
  Attaching package: 'SentimentAnalysis'
  
  The following object is masked from 'package:base':
  
      write
  
  > 
  > test_check("SentimentAnalysis")
  Comparing: wordlist vs wordlist
  
  Total unique words: 5
  Matching entries: 1 (0.2%)
  Comparing: binary vs binary
  
  Total unique words: 10
  Matching entries: 3 (0.3%)
  Entries with same classification: 2 (0.2%)
  Entries with different classification: 1 (0.1%)
  Comparing: weighted vs weighted
  
  Total unique words: 10
  Matching entries: 3 (0.3%)
  Entries with same classification: 2 (0.2%)
  Entries with different classification: 1 (0.1%)
  Correlation between scores of matching entries: 0.5
  Average sentiment: 0.25 vs -0.4
  -- 1. Failure: dictionary generations works correctly (@test.generateDictionary.
  dictionary$scores not equal to c(-0.4190744, 0.3955698).
  2/2 mismatches (average diff: 0.0711)
  [1] -0.344 - -0.419 == 0.0746
  [2]  0.463 -  0.396 == 0.0675
  
  == testthat results  ===========================================================
  OK: 386 SKIPPED: 0 FAILED: 1
  1. Failure: dictionary generations works correctly (@test.generateDictionary.R#63) 
  
  Error: testthat unit tests failed
  Execution halted
File 'sequoia/libs/i386/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.o'
File 'sequoia/libs/x64/sequoia.dll':
  Found '_gfortran_st_write', possibly from 'write' (Fortran), 'print'
    (Fortran)
    Object: 'sequoia.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
Authors@R field gives persons with no valid roles:
  Engineering and Physical Sciences Research Council [fnd] (EPSRC programme grant ref: EP/L014165/1)
Found the following significant warnings:
  Warning: D:/temp/RtmpCowpeK/R.INSTALL1b7207d1d3c8f/sharpr2/man/sharpr2-package.Rd:1: All text must be in a section
See 'd:/Rcompile/CRANpkg/local/3.3/sharpr2.Rcheck/00install.out' for details.
prepare_Rd: sharpr2-package.Rd:1: All text must be in a section
installed size is  7.4Mb
  sub-directories of 1Mb or more:
    www   6.2Mb
Missing or unexported object: 'spatstat::overlap.xypolygon'
Running examples in 'SIBER-Ex.R' failed
The error most likely occurred in:

> ### Name: maxLikOverlap
> ### Title: Calculate the overlap between two ellipses based on the maximum
> ###   likelihood fitted ellipses.
> ### Aliases: maxLikOverlap
> 
> ### ** Examples
> 
> # load in the included demonstration dataset data("demo.siber.data")
> siber.example <- createSiberObject(demo.siber.data) 
> 
> # The first ellipse is referenced using a character string representation 
> # where in "x.y", "x" is the community, and "y" is the group within that 
> # community.
> ellipse1 <- "1.2" 
> 
> # Ellipse two is similarly defined: community 1, group3 
> ellipse2 <- "1.3"
> 
> # the overlap betweeen the corresponding 95% prediction ellipses is given by: 
> ellipse95.overlap <- maxLikOverlap(ellipse1, ellipse2, siber.example,
+ p.interval = 0.95, n = 100)
Error: 'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Error in re-building vignettes:
  ...
Warning in buildVignettes(dir = "d:/Rcompile/CRANpkg/local/3.3/SIBER.Rcheck/vign_test/SIBER") :
  Files named as vignettes but with no recognized vignette engine:
   'vignettes/test-nonnumeric-community-labels.Rmd'
   'vignettes/test-nonnumeric-group-labels.Rmd'
(Is a VignetteBuilder field missing?)
Quitting from lines 89-115 (Ellipse-Overlap.Rmd) 
Error: processing vignette 'Ellipse-Overlap.Rmd' failed with diagnostics:
'overlap.xypolygon' is not an exported object from 'namespace:spatstat'
Execution halted
Running 'testthat.R' [24s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    |============================                                          |  40%
    |                                                                            
    |==========================================                            |  60%[1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  NA"
  [1] "Estimated replications per hour:  230769"
  [1] "Estimated replications per hour:  2307697"
  [1] "Estimated replications per hour:  256412"
  [1] "Estimated replications per hour:  2307838"
  [1] "Estimated replications per hour:  256412"
  == testthat results  ===========================================================
  OK: 63 SKIPPED: 0 FAILED: 1
  1. Failure: summary.fun can handel logical data and returning vector 
  
  Error: testthat unit tests failed
  Execution halted
Running 'test_scripts.R' [26s]
Running the tests in 'tests/test_scripts.R' failed.
Last 13 lines of output:
  > print(gam(log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
  +     data = mackerel))
  Call:
  gam(formula = log(Density) ~ lo(log(mack.depth)) + lo(Temperature), 
      data = mackerel)
  
  Degrees of Freedom: 278 total; 270.9924 Residual
  Residual Deviance: 335.5316 
  
  > par(mfrow = c(2, 2))
  
  > plot.gam(model1, se = TRUE)
  Error in eval(expr, envir, enclos) : could not find function "plot.gam"
  Calls: source -> withVisible -> eval -> eval
  Execution halted
contact_matrix: possible error in xtabs(data = contacts.sample, formula
  = weight ~ agegroup + cnt.agegroup, addNA = TRUE): unused argument
  (addNA = TRUE)
contact_matrix: possible error in xtabs(data = part.sample, formula =
  weight ~ agegroup, addNA = TRUE): unused argument (addNA = TRUE)
Running examples in 'socialmixr-Ex.R' failed
The error most likely occurred in:

> ### Name: contact_matrix
> ### Title: Generate a contact matrix from diary survey data
> ### Aliases: contact_matrix
> 
> ### ** Examples
> 
> data(polymod)
> contact_matrix(polymod, countries = "United Kingdom", age.limits = c(0, 1, 5, 15))
Using Polymod Social Contact Data. To cite this in a publication, use the 'cite' function
Sampling the age of contacts with missing age from other participants of the same age group.
  To change this behaviour, set the 'missing.contact.age' option
Error in xtabs(data = contacts.sample, formula = weight ~ agegroup + cnt.agegroup,  : 
  unused argument (addNA = TRUE)
Calls: contact_matrix -> xtabs
Execution halted
Running 'testthat.R' [14s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
    @Misc{,
      title = {Polymod Social Contact Data},
      author = {Joël Mossong and Niel Hens and Mark Jit and Philippe Beutels and Kari Auranen and Rafael Mikolajczyk and Marco Massari and Stefania Salmaso and Gianpaolo Scalia Tomba and Jacco Wallinga and Janneke Heijne and Malgorzata Sadkowska-Todys and Magdalena Rosinska and W. John Edmunds},
      doi = {10.5281/zenodo.1059920},
      publisher = {Zenodo},
      note = {Version 1.1},
      year = {2017},
    }
  
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 1
  1. Error: (unknown) (@test-matrix.r#13) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 57-58 (introduction.Rmd) 
Error: processing vignette 'introduction.Rmd' failed with diagnostics:
unused argument (addNA = TRUE)
Execution halted
rmvn.sparse: no visible global function definition for 'rnorm'
rmvn.sparse: no visible global function definition for 'as'
Undefined global functions or variables:
  as rnorm
Consider adding
  importFrom("methods", "as")
  importFrom("stats", "rnorm")
to your NAMESPACE file (and ensure that your DESCRIPTION Imports field
contains 'methods').
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/sparsesvd.Rcheck/00install.out' for details.
installed size is 15.8Mb
  sub-directories of 1Mb or more:
    R      4.0Mb
    doc    4.7Mb
    help   4.9Mb
    libs   1.2Mb
Warning: invalid input found on input connection 'stability-Ex.R'
installed size is  6.9Mb
  sub-directories of 1Mb or more:
    doc       1.1Mb
    extdata   5.0Mb
Running examples in 'stocks-Ex.R' failed
The error most likely occurred in:

> ### Name: twometrics_graph
> ### Title: Graph One Performance Metric vs. Another for Various Investments
> ### Aliases: twometrics_graph
> 
> ### ** Examples
> 
> # Plot annualized growth vs. maximum drawdown for VFINX, SSO, and UPRO
> fig <- twometrics_graph(tickers = c("VFINX", "SSO", "UPRO"))
Error in 1:loc.end : argument of length 0
Calls: twometrics_graph -> load_gains
Execution halted
Authors@R field gives persons with no valid roles:
  Scott  Chamberlin [rev] (Scott reviewed the package for rOpenSci, see https://github.com/ropensci/onboarding/issues/10)
installed size is  5.9Mb
  sub-directories of 1Mb or more:
    data   1.9Mb
    doc    2.6Mb
Running examples in 'survtmle-Ex.R' failed
The error most likely occurred in:

> ### Name: plot.tp.survtmle
> ### Title: Plot Results of Cumulative Incidence Estimates
> ### Aliases: plot.tp.survtmle
> 
> ### ** Examples
> 
> library(survtmle)
> set.seed(341796)
> n <- 100
> t_0 <- 10
> W <- data.frame(W1 = runif(n), W2 = rbinom(n, 1, 0.5))
> A <- rbinom(n, 1, 0.5)
> T <- rgeom(n,plogis(-4 + W$W1 * W$W2 - A)) + 1
> C <- rgeom(n, plogis(-6 + W$W1)) + 1
> ftime <- pmin(T, C)
> ftype <- as.numeric(ftime == T)
> suppressWarnings(
+   fit <- survtmle(ftime = ftime, ftype = ftype,
+                   adjustVars = W, glm.ftime = "I(W1*W2) + trt + t",
+                   trt = A, glm.ctime = "W1 + t", method = "hazard",
+                   verbose = TRUE,  t0 = t_0, maxIter = 2)
+ )
> tpfit <- timepoints(fit, times = seq_len(t_0))
> plot(tpfit)
Error in `colnames<-`(`*tmp*`, value = c("t", "group", "value")) : 
  'names' attribute [3] must be the same length as the vector [2]
Calls: plot -> plot.tp.survtmle -> colnames<-
Execution halted
Package suggested but not available for checking: 'tidyquant'
Running 'testthat.R' [2s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 11
  1. Error: (unknown) (@test_sw_sweep.R#3) 
  2. Error: (unknown) (@test_tidiers_StructTS.R#3) 
  3. Error: (unknown) (@test_tidiers_arima.R#3) 
  4. Error: (unknown) (@test_tidiers_bats_tbats.R#3) 
  5. Error: (unknown) (@test_tidiers_decomposed_ts.R#3) 
  6. Error: (unknown) (@test_tidiers_ets.R#3) 
  7. Error: (unknown) (@test_tidiers_hw.R#3) 
  8. Error: (unknown) (@test_tidiers_lm.R#3) 
  9. Error: (unknown) (@test_tidiers_nnetar.R#3) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-30 (SW00_Introduction_to_sweep.Rmd) 
Error: processing vignette 'SW00_Introduction_to_sweep.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
Packages required and available but unsuitable versions:
  'parallel' 'phyloseq' 'ShortRead'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Authors@R field gives persons with no valid roles:
  Luke Winslow [rev] (Reviewed for rOpenSci)
  Laura DeCicco [rev] (Reviewed for rOpenSci)
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  12: shannon_entropy(.)
  13: reduce_data(.data, !(!enquo(X)), numvars = 1, na.rm = na.rm)
  14: tidyselect::vars_select(names(reduced_tab), !(!(!quos(...))))
  15: vars_select_eval(.vars, quos)
  16: map_lgl(quos, quo_is_helper)
  17: .f(.x[[i]], ...)
  18: extract_expr(quo)
  19: is_call(expr, paren_sym)
  
  == testthat results  ===========================================================
  OK: 37 SKIPPED: 0 FAILED: 1
  1. Error: right number of columns given (@test-errors.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Package required but not available: 'alphavantager'

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

> ### Name: tk_augment_timeseries
> ### Title: Augment the time series signature to the data
> ### Aliases: tk_augment_timeseries tk_augment_timeseries_signature
> 
> ### ** Examples
> 
> library(tidyquant)
Error in library(tidyquant) : there is no package called 'tidyquant'
Execution halted
Running 'testthat.R' [3s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  
  == testthat results  ===========================================================
  OK: 0 SKIPPED: 0 FAILED: 9
  1. Error: (unknown) (@test_tk_augment_timeseries.R#2) 
  2. Error: (unknown) (@test_tk_get_timeseries.R#2) 
  3. Error: (unknown) (@test_tk_index.R#3) 
  4. Error: (unknown) (@test_tk_make_future_timeseries.R#2) 
  5. Error: (unknown) (@test_tk_tbl.R#6) 
  6. Error: (unknown) (@test_tk_ts.R#4) 
  7. Error: (unknown) (@test_tk_xts.R#4) 
  8. Error: (unknown) (@test_tk_zoo.R#4) 
  9. Error: (unknown) (@test_tk_zooreg.R#4) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 16-29 (TK00_Time_Series_Coercion.Rmd) 
Error: processing vignette 'TK00_Time_Series_Coercion.Rmd' failed with diagnostics:
there is no package called 'tidyquant'
Execution halted
installed size is 22.5Mb
  sub-directories of 1Mb or more:
    examples  19.2Mb
    include    2.9Mb
Package required but not available: 'rsolr'

See section 'The DESCRIPTION file' in the 'Writing R Extensions'
manual.
Running 'Coxph-Ex.R' [3s]
Running the tests in 'tests/Coxph-Ex.R' failed.
Complete output:
  > 
  > library("tram")
  Loading required package: mlt
  Loading required package: basefun
  Loading required package: variables
  > library("survival")
  > library("trtf")
  Error in library("trtf") : there is no package called 'trtf'
  Execution halted
Error in re-building vignettes:
  ...
Attaching package: 'TH.data'

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

    geyser

Loading required package: SparseM

Attaching package: 'SparseM'

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

    backsolve


Attaching package: 'quantreg'

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

    untangle.specials

Quitting from lines 22-51 (tram.Rnw) 
Error: processing vignette 'tram.Rnw' failed with diagnostics:
there is no package called 'trtf'
Execution halted
installed size is  5.4Mb
  sub-directories of 1Mb or more:
    doc    2.7Mb
    libs   1.4Mb
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/treethresh.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uaparserjs.Rcheck/00install.out' for details.
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  1/1 mismatches
  [1] 10 - 9 == 1
  
  -- 2. Failure: random content can be retrieved (@test_udapi.R#10)  -------------
  `x` not equal to `expected`.
  1/1 mismatches
  [1] 10 - 9 == 1
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 2
  1. Failure: specific content can be retrieved (@test_udapi.R#5) 
  2. Failure: random content can be retrieved (@test_udapi.R#10) 
  
  Error: testthat unit tests failed
  Execution halted
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3new/uroot.Rcheck/00install.out' for details.
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/uwIntroStats.Rcheck/00install.out' for details.
installed size is  6.3Mb
  sub-directories of 1Mb or more:
    R      1.5Mb
    doc    1.2Mb
    help   2.6Mb
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 8 SKIPPED: 0 FAILED: 15
  1. Failure: Variable importance (@test_iris.R#15) 
  2. Failure: Variable importance (@test_iris.R#18) 
  3. Failure: OOB erros of nested models (@test_iris.R#25) 
  4. Failure: OOB erros of nested models (@test_iris.R#28) 
  5. Failure: Thresholds for the 3 steps (@test_iris.R#34) 
  6. Failure: Thresholds for the 3 steps (@test_iris.R#36) 
  7. Failure: Thresholds for the 3 steps (@test_iris.R#38) 
  8. Failure: Variable importance (@test_orange.R#16) 
  9. Failure: Variable importance (@test_orange.R#20) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
File 'waffect/libs/i386/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'
File 'waffect/libs/x64/waffect.dll':
  Found 'rand', possibly from 'rand' (C)
    Object: 'waffect.o'

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

See 'Writing portable packages' in the 'Writing R Extensions' manual.
installed size is  9.7Mb
  sub-directories of 1Mb or more:
    doc    2.2Mb
    libs   7.3Mb
Running 'testthat.R' [5s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  == testthat results  ===========================================================
  OK: 26 SKIPPED: 0 FAILED: 18
  1. Error: canCallChrome (@test-chrome.R#3) 
  2. Error: pickUpErrorFromReturnCode (@test-chrome.R#43) 
  3. Error: pickUpErrorFromPortInUse (@test-chrome.R#62) 
  4. Error: canCallGecko (@test-gecko.R#4) 
  5. Error: pickUpErrorFromReturnCode (@test-gecko.R#44) 
  6. Error: pickUpErrorFromPortInUse (@test-gecko.R#63) 
  7. Error: canCallIEDriver (@test-iedriver.R#4) 
  8. Error: pickUpErrorFromReturnCode (@test-iedriver.R#46) 
  9. Error: pickUpErrorFromPortInUse (@test-iedriver.R#68) 
  1. ...
  
  Error: testthat unit tests failed
  Execution halted
Running examples in 'WufooR-Ex.R' failed
The error most likely occurred in:

> ### Name: fields_info
> ### Title: Return details about form's fields
> ### Aliases: fields_info
> 
> ### ** Examples
> 
> fields_info(formIdentifier = "z5kqx7h1gtvg4g", showRequestURL = TRUE)
Error in http_statuses[[as.character(status)]] : subscript out of bounds
Calls: fields_info -> doRequest -> stop_for_status
Execution halted
Running 'testthat.R' [6s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  3: stop_for_status(getResponse)
  4: stop(http_condition(x, "error", task = task, call = call))
  5: http_condition(x, "error", task = task, call = call)
  6: http_status(status)
  
  == testthat results  ===========================================================
  OK: 1 SKIPPED: 0 FAILED: 5
  1. Error: Fields request returns 17 rows, always (@test-fieldsAndreports.R#9) 
  2. Error: Reports have 11 fields (@test-fieldsAndreports.R#16) 
  3. Error: Form request returns 17 rows, always (@test-forms.R#9) 
  4. Error: Form returns entries, with the requested URL (@test-forms.R#14) 
  5. Error: User request returns 17 rows, always (@test-users.R#9) 
  
  Error: testthat unit tests failed
  Execution halted
Error in re-building vignettes:
  ...
Quitting from lines 46-47 (Tutorial.Rmd) 
Error: processing vignette 'Tutorial.Rmd' failed with diagnostics:
subscript out of bounds
Execution halted
Package suggested but not available for checking: 'GenomicScores'
installed size is 19.0Mb
  sub-directories of 1Mb or more:
    java  19.0Mb
Running 'testthat.R' [1s]
Running the tests in 'tests/testthat.R' failed.
Last 13 lines of output:
  y[1]: "# ç\u008f¾è¡ã\u0081®å­¦æ ¡ææ³ã\u0081§ã\u0081¯ã\u0081è±èªã\u0081«ã\
  y[1]: u0081ããã\u0081ã\u0081ªãç®çèªã\u008dãè£èªã\u008d"
  
  -- 2. Failure: UTF-8 is OK (@test.R#78)  ---------------------------------------
  length(op) not equal to 1.
  1/1 mismatches
  [1] 0 - 1 == -1
  
  == testthat results  ===========================================================
  OK: 14 SKIPPED: 0 FAILED: 2
  1. Failure: UTF-8 is OK (@test.R#66) 
  2. Failure: UTF-8 is OK (@test.R#78) 
  
  Error: testthat unit tests failed
  Execution halted
newXMLDoc: no visible binding for global variable 'doc'
xmlFlatListTree : f: no visible binding for global variable 'nodeNames'
xmlFlatListTree : f: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeSet'
xmlFlatListTree : addNode: no visible binding for global variable 'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for global variable
  'nodeNames'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'idx'
xmlFlatListTree : addNode: no visible binding for '<<-' assignment to
  'parentCount'
xmlFlatListTree : addNode: no visible binding for global variable
  'parentCount'
xmlFlatListTree : <anonymous>: no visible binding for global variable
  'e'
xmlFlatTree : <anonymous>: no visible binding for global variable 'e'
Undefined global functions or variables:
  doc e idx nodeNames nodeSet parentCount
Installation failed.
See 'd:/Rcompile/CRANpkg/local/3.3/xptr.Rcheck/00install.out' for details.
Running examples in 'yCrypticRNAs-Ex.R' failed
The error most likely occurred in:

> ### Name: annotationsSet
> ### Title: Create a geneAnnotation object.
> ### Aliases: annotationsSet
> 
> ### ** Examples
> 
> annotationsSet()
Error in useDataset(mart = mart, dataset = dataset, verbose = verbose) : 
  The given dataset:  scerevisiae_gene_ensembl , is not valid.  Correct dataset names can be obtained with the listDatasets function.
Calls: annotationsSet -> <Anonymous> -> useDataset
Execution halted